Sandwalk: May 2009

Sunday, May 31, 2009

Another Blogger Leaves the SEED Blogs (ScienceBlogs.con)

Dr. Joan Bushwell's Chimpanzee Refuge is the latest blog to jump ship. That makes three or four blogs that have left the SEED group in the past few weeks. Most of them have been fairly cryptic about their reasons for leaving but Kevin Beck hints at something sinister happening behind the scenes [Bon(obo) voyage: the chimps are loping away from ScienceBlogs.com].

I also want to be open about what I say without fear of being castigated as a misogynist (a term often used inaccurately - try "sexist," folks), a tremendously ironic notion given that I harbor genuine ovaries (although going dormant) and had some pretty hair-raising experiences during my fairly long scientific career which allow me to speak from a solid platform of experience and credibility.

The latter sniping derives from my stumbling upon some very shoddy behavior in the back rooms of Science Blogs, stuff that removed any doubt that leaving Science Blogs for an independent venue was the thing to do. The majority of the folks that blog here do not participate in this -- uh -- "community" forum, but the ones who do are fairly heavy hitters and like it or not, they set a tone.

Does anyone out there want to explain this? What's going on n the back rooms of ScienceBlogs?

Saturday, May 30, 2009

John Hawks on "Adaptationists vs Pluralists"

John Hawks recently posted a comment about adaptationists [see Richard Lewontin: "[T]oo rapid for genetic adaptation"].

Hawks said ...

I don't really find the "pluralist versus adaptationist" debate very interesting. Despite the vocal complaints of some, I can't ever seem to locate the mythical "adaptationists" who deny that non-adaptive evolution ever happens. So the "debate" always comes down to whether particular adaptive hypotheses are true. Since no scientific hypothesis is true a priori, and since "those adaptationists are always saying stupid things" is not a scientific argument, I don't see the point.

I'm astonished that, after all these years, the adaptationists still don't get it.

First, the mythical adaptationist is a straw man that only exists in the minds of the adaptionists. This particular straw man was easily disposed of in the original Spandrel's paper. It is only resurrected by those who haven't been paying attention

Second, the debate does not come down to "whether adaptive hypotheses are true." It comes down to whether any adaptive hypothesis is true. When speculating on mechanisms, adaptationists tend to ignore any mechanism of evolution other than natural selection That's the problem. As a general rule, they don't seriously consider the possibility that the correct explanation may not be adaptation.

It's a difference in worldviews. Pluralists tend to look at an evolutionary outcome and ask, "What mechanism of evolution caused this?" Adaptationists tend to look at the same outcome and ask, "How can this be explained by natural selection?" Adaptationists know about random genetic drift—they just don't think it's an important player when it comes to the parts of evolution that they're interested in. I think that's a bad assumption.

Friday, May 29, 2009

The Mouse Genome is "Finished"

The first draft of the mouse genome was published by the Mouse Genome Sequencing Consortium back in 2002. At the time it was the only available non-human genome sequence. Since then several dozen other draft sequences have been published and many more are in progress. You can view a complete list at NCBI: Mammalian Genomes.

A finished version of the human genome sequence was published a few years ago and up until this month it was the only one listed as "complete." Now you can add the Mus musculus (mouse) genome to the list of complete publicly available genome sequences (Church et al. 2009).

When scientists say that a genome is complete or "finished" they don't really mean it. What they mean is that the effort has reached the point of diminishing returns. They are confident that they have found almost all of the genes and most of the important bits but they're well aware of the fact that some parts of the genome are missing.

This figure from the Church et al. paper illustrates the extent of a "finished" sequence. The green chromosomes represent the original draft sequence. Unsequenced regions are shown in black. As you can see, there were many gaps in the original sequence—176,000 to be exact.

The blue chromosomes represent the "finished" genome sequence. There are a lot fewer black regions and they are mostly confined to the centromeres/telomeres at the top ends of the chromsomes. As is the case with the human genome, these regions are mostly repetitive DNA that resists assembly into large blocks [The Human Genome Sequence Is not Complete].

The reason why the Y chromosome is missing is because it was a female genome that was sequenced.

Mice have 19 autosomes (non-sex chromosomes, see karyotype above). When you compare the mouse and human genomes you can see right away that the sequences of chromosomes aren't conserved. What is conserved are large blocks of sequence that may be found on one particular mouse chromosome but on a completely different human chromosome.

The mapping of these conserved synteny relationships reveals a great deal about the evolution of human and mouse chromosomes from a common ancestor. For example, the yellow block of sequence at the tip of human chromosome 1 (below) is found on mouse chromosome 4. The other parts of mouse chromosome 4 are found on human chromosome 6, 8, and 9.

What this means is that there are large blocks of genes that have been preserved since the time of the common ancestor. There are 334 chromosomal breakpoints that define the blocks of homologous sequence between human and mouse. The rearrangements took place in both lineages and the frequency of such rearrangements seems to be similar in most mammalian lineages.

The current "build" of the mouse genome has 20,210 protein-encoding genes. This is a substantial reduction from the 22,011 genes predicted in the initial draft sequence. As a general rule, the number of confirmed genes declines with each improvement in the sequence. This is mostly due to the joining together of gene fragments that were misidentified in the first draft. The authors note that 30% of the genes in the "finished" sequence were disrupted by errors and gaps in the first draft. Some new genes are added because of the addition of new sequence data but this doesn't compensate for the genes that are removed.

A total of 2,185 new genes were added. Most of them are duplicates of genes previously identified in the original draft sequence. In fact, the biggest change in the "finished" sequence is the identification of 126,000 Kb (126Mb) of duplicated sequences that were not detected in the first draft. This makes the mouse genome—with about 5% of segmentally duplicaed sequence—similar to the human genome. Initially there were hardly any duplicated regions in the mouse genome leading to speculation that duplications were much more common in primates.

Almost half of the duplicated regions exhibit different copy numbers in various strains of mice. Since the sequenced genome comes from a highly inbred line of laboratory mice (C57BL/6J), it is possible that the o0bserved copy number differs substantially from wild-type mice.

The human genome has 19,042 protein-encoding genes. Of these 15,187 (80%) have clear orthologs in the mouse genome. (Orthologs are homologous genes in the same location. They are related by descent from a common ancestor.) The orthologous genes represent 75% of the mouse genes. Most of the remaining genes are not novel genes but duplicates of the orthologs.

Surprisingly, there were only 12,845 orthologous genes in the first draft sequence. The difference is due to the identification of mistakes in the earlier data where sequence and assembly errors led to the misidentification of conserved genes. What this means is that a substantial number of papers comparing humans and mouse genomes will need to be re-evaluated. Here's how the authors put it ...

The shortcomings of the initial draft assembly are readily apparent now that a more-complete genome assembly is available. Undoubtedly these have led to incomplete or inaccurate understanding of some aspects of mouse biology. The availability of high quality genome sequence for the mouse will lead the way in dismissing some commonly held misconceptions and, more importantly, in revealing many previously hidden secrets of mouse biology.

The total length of protein-encoding exons in the mouse genome is 33,500 Kb (33.5 Mb). The revised genome size is 2,660,000 Kb (2.66 Gb). Thus, protein-encoding regions represent only 1.3% of the genome. This is similar to the value in the human genome (1.1% or 32.6 Mb out of 3.08 Gb).

There are many important non-coding sequences including centromeres, telomeres, origins of replication, scaffold attachment regions etc. All genes have substantial regulatory regions that aren't counted in the 1.3% of the genome that encodes protein. In addition, there are hundreds of tRNA genes, ribosomal RNA genes, and genes for essential small RNAs.

Nevertheless, a substantial proportion of the mouse genome (>90%) appears to be junk DNA with no known function. Most of it (~50%) consist of active and degenerate transposons similar to the LINES and SINES found in all other mammalian genomes.

[Photo Credit: Oak Ridge National Laboratory]

Church, D.M., Goodstadt, L., Hillier, L.W., Zody, M.C., Goldstein, S., et al. (2009) Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biol 7(5): e1000112. [doi:10.1371/journal.pbio.1000112 ]

Thursday, May 28, 2009

A Nomination Meeting

Last Fall I joined the Liberal Party of Canada in order to have a say in electing a new leader and a new candidate in my riding. My riding is Mississauge-Erindale in the city of Mississauga, just west of Toronto, Ontario, Canada.

The candidate in the last election was Omar Alghabra, who at the time was the sitting member of the House of Commons in Ottawa. He lost the election by 400 votes.

Well, as it turns out, I didn't get a chance to vote for a new leader. The new leader, Michael Ingatieff, was acclaimed when when eveyone else dropped out of the race last December.

I looked forward to a healthy debate on choosing a candidate in my riding.

I received a notice in the mail on May 12th stating that there would be a nomination meeting in two weeks. All nomination forms must be received by the Liberal Party office in Toronto on May 18th at the latest. That left six days, counting Saturday and Sunday, to fill out a raft of forms [Nomination Rules].

The meeting was last night and the only candidate was Omar Alghabra. I took a picture of him on my cell phone at the meeting. I was told by the riding Chair that no other candidates would have been permitted but it was a moot point since the system was set up in such a way that it would have been almost impossible to get another nomination in on time.

This doesn't seem very democratic and it seems inconsistent with the openness that the Liberal Party desires. I don't know if Omar would have been nominated anyway but what I do know is that I would have been a lot happier if there had been some debate and discussion about choosing a person who could win the next election.

I feel that I've been manipulated. I wasn't the only one at the meeting who felt that way.

It's going to be hard to get excited about working for Omar during the upcoming campaign. The whole idea behind openness and democracy is to let everyone have their say. When that happens, people feel they're part of the process and they're willing to work with the system no matter which candidate is chosen to run in a riding. Competition and debate are healthy. Secrecy and manipulation are not.

Nobel Laureate: Willem Einthoven

The Nobel Prize in Physiology or Medicine 1924

"for his discovery of the mechanism of the electrocardiogram"

Willem Einthoven (1860 - 1927) won the Noble Prize in 1924 for discovering a practical machine for detecting the electrical actions of the heart. He discovered the electrocardiogram and identified its characteristic features.

Einthoven's apparatus was based on the string galvanometer, which he had developed a number of years earlier. The importance of an accurate electrocardiogram in diagnosing various heart conditions was instantly recognized. But first, the actions of a normal heart had to be carefully recorded and explained. The explanation put forth by Einthoven proved to be substantially correct.

Here's how the standard electrocardiogram is described in the Presentation Speech.
THEME:
Nobel Laureates

However, in his work in 1908 Einthoven gave an interpretation of the electrocardiogram. He starts from the fact that the stimulus (of the contraction process, the «negativity») is propagated as a wave in the muscular system of the heart. The string of the galvanometer, connected with the heart in a closed circuit in one of the usual ways, remains in the original position not only when the heart is at rest, but also when the «negativity» of the assemblage of points of the heart wall show the same value. A deflection is therefore in the first place to be expected at the beginning and at the end of a systole, and it presupposes that the condition of activity does not occur, respectively cease, simultaneously in all elements of the muscle. Further: if the contraction process (the stimulus) is propagated symmetrically in relation to the points connected to the galvanometer, then no deflection would take place either. Under such circumstances the electrocardiogram must be determined partly by the starting-point of the stimulus to the heart beat, partly by the conduction system within the heart. The point of departure for the normal heart beat has been sufficiently well known since the middle of the 1890's, the bundle of His also since that time, and Tawara's description of the ramification of the conduction system inside the ventricles known since 1906. According to Einthoven the P-peak is an expression of the propagation of the stimulus wave in the muscular system of the auricle. The negativity wave, corresponding to the stimulus wave in the His-Tawara system, is considered too weak by Einthoven to cause any deflection in the galvanometer. The QRS-complex is determined by the propagation of the stimulus wave in the muscular system of the two ventricles, proceeding in unsymmetrical fashion to the points of lead, starting at different moments at the transition of the tree-like ramified Purkinje's fibres into the various parts of the proper muscular system of the heart. When the contraction process has reached its maximum in all the points of the ventricular wall, the string returns to its original position. When the contraction ceases in the various parts at different moments, a T-peak is obtained.

It is unnecessary in this connection to consider the interpretations proposed by other investigators, as Einthoven's concept is the only one which has proved to be tenable. The interpretation that the P-peak belongs to the auricular systole is mainly based on his observation of electrocardiograms in cases of heart block in patients or during vagus stimulation in dogs. With regard to the interpretation of the QRS-complex Einthoven was evidently the first who has clearly recognized the significance of the conduction system in this connection. The train of thought in the interpretation of the T-peak can already be detected in Burdon-Sanderson's previously mentioned work.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Mixing Science, Religion, and Politics

The first draft of the human genome sequence was announced on June 26, 2000. There was a huge press conference in the East Room of the White House with Craig Venter, President Bill Clinton, and Francis Collins. British Prime Minister Tony Blair appeared via videolink from London.

The event is recounted on pages 2 & 3 of Francis Collins' book The Language of God. It's worth recalling because it reminds Americans of what they can expect if Collins were to become head of NIH.

But the most important part of his speech that most attracted public attention jumped from the scientific perspective to the spiritual. "Today," [Clinton] said, "we are learning the language in which God created life. We are gaining ever more awe for the complexity, the beauty, and the wonder of God's most divine and sacred gift."

Was I, a rigorously trained scientist, taken aback at such a blatantly religious reference by the leader of the free world at a moment such as this? Was I tempted to scowl or look at the floor in embarrassment? No, not at all. In fact I had worked closely with the president's speechwriter in the frantic days just prior to this announcement, and had strongly endorsed the inclusion of this paragraph. When it came time for me to add a few words of my own, I echoed this sentiment: "It's a happy day for the world. It is humbling for me, and awe-inspiring, to realize that we have caught the first glimpse of our own instruction book, previously known only to God."

What was going on here? Why would a president and a scientist, charged with announcing a milestone in biology and medicine, feel compelled to invoke a connection with God? Aren't the scientific and spiritual worldviews antithetical, or shouldn't they at lest avoid appearing in the East Room together? What were the reasons for invoking God in those two speeches? Was this poetry? Hypocrisy? A cynical attempt to curry favor from believers, or to disarm those who might criticize this study of the human genome as reducing humankind to machinery? No. Not for me. Quite the contrary, for me the experience of sequencing the human genome, and uncovering this most remarkable of all texts, was both a stunning scientific achievement and an occasion of worship.

Wednesday, May 27, 2009

Faith and Evolution at the Discovery Institute

The Discovery Institute has a new website called Faith + Evolution. It's designed to explore the relationship, if any, between the Christian faith and science.

Prominently featured on the home page is an article by Jonathan Wells.

Is Francis Collins Right about Evolution?

Francis Collins feels that intelligent design poses a serious problem to Christian belief because it rejects Darwinian evolution, which he feels is supported by overwhelming evidence. But the only evidence Collins cites for Darwin’s mechanism of variation and selection is microevolution—minor changes within existing species. And the principal evidence he cites for Darwin’s claim of common ancestry is DNA sequences that he says have no function—though genome researchers are discovering that many of them do have functions.

Collins’s defense of Darwinian theory turns out to be largely an argument from ignorance that must retreat as we learn more about the genome—in effect, a Darwin of the gaps.

Wells is referring to the evidence of shared pseudogenes and other genomic signatures of common descent. This won't do, according to Wells. Collins is not one of the good guys.

I wonder if Jonathan Wells has read a book called The Edge of Evolution? It was published in 2007. The author is Michael Behe—a Senior Fellow at the Discovery Institute.

Behe also describes the evidence from pseudogenes. Here's an excerpt from pages 70-71.

When two lineages share what appears to be an arbitrary genetic accident, the case for common descent becomes compelling, just as the case for plagiarism becomes overpowering when one writer makes the same unusual misspellings of another, within a copy of the same words. That sort of evidence is seen in the genomes of chimps and chimpanzees. For example, both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C. As a result, neither humans nor chimps can make their own vitamin C. If an ancestor of the two species originally sustained the mutation and then passed it to both descendant species, that would neatly explain the situation.

More compelling evidence for the shared ancestry of humans and other primates comes from their hemoglobin—not just their working hemoglobin, but a broken hemoglobin gene, too. .... In the region between the two gamma genes and a gene that works after birth, human DNA contains a broken gene (called a "psedugoene") that closely resembles a working gene for a beta chain, but has features in its sequence that preclude it from coding successfully for a protein.

Chimp DNA has a very similar pseudogene at the same position. The beginning of the human pseudogene has two particular changes in two nucleotides that seem to deactivate the gene. The chimp pseudogene has the exact same changes. A bit further down in the human pseudogene is a deletion mutation, where one particular letter is missing. For technical reasons, the deletion irrevocably messes up the gene's coding. The very same letter is missing in the chimp gene. Toward the end of the human pseduogene another letter is missing. The chimp pseudogene is missing it, too.

The same mistakes in the same gene in the same positions of both human and chimp DNA. If a common ancestor first sustained the mutational mistakes and subsequently gave rise to those two modern species, that would very readily account for why both species have them now. It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans.

That strong evidence from the pseudogene points well beyond the ancestry of humans. Despite some remaining puzzles, there's no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.

Behe and Collins are on the same page. They both recognize the powerful genetic evidence of common descent (macroevolution).

I wonder if Jonathan Wells and Michael Behe talk to each other? I'd love to be a fly on the wall.

Francis Collins and the National Institutes of Health (USA)

After many years of service as director of the National Human Genome Research Institute (NHGRI), Francis Collins resigned from NIH last year. His reasons for quitting were widely reported in the media. Here's the press release from NIH [Francis S. Collins to Step Down as Director of National Human Genome Research Institute].

Dr. Collins explained that his decision to step down as leader of NHGRI came after much personal deliberation. "My decision was driven by a desire for an interval of time dedicated to writing, reflection and exploration of other professional opportunities in the public or private sectors," he said. "The demands and responsibilities of directing an NIH institute do not allow the time commitment necessary for this. In addition, I may need greater latitude than my current position allows to pursue other potential positions of service without encountering any possible conflicts of interest, whether real or perceived."

We now know that the "real or perceived" conflict of interest relates to the creation of The BioLogos Foundation. Here's the mission statement.

Dr. Francis Collins established The BioLogos Foundation to address the escalating culture war between science and faith in the United States. On one end of the spectrum, “new atheists” argue that science removes the need for God. On the other end, religious fundamentalists argue that the Bible requires us to reject much of modern science. Many people - including scientists and believers in God - do not find these extreme options attractive.

BioLogos represents the harmony of science and faith. It addresses the central themes of science and religion and emphasizes the compatibility of Christian faith with scientific discoveries about the origins of the universe and life. To communicate this message to the general public and add to the ongoing dialog, The BioLogos Foundation created BioLogos.org.

Funded by a grant from the John Templeton Foundation, the Web site is a reliable source of scholarly thought on contemporary issues in science and faith that highlights the compatibility of modern science with traditional Christian beliefs. BioLogos.org features responses to a myriad of questions received by Collins, author of The Language of God, Karl Giberson, author of Saving Darwin, and Darrel Falk, author of Coming to Peace With Science since the publication of their books.

It's pretty obvious why running such a foundation is not compatible with a leadership role at the National Institutes of Health (NIH).

That's what makes this report in Scientific American so disturbing [Former Human Genome Project leader Francis Collins likely next NIH director].

The National Institutes of Health (NIH) will likely bring on geneticist Francis Collins, leader of the Human Genome Project, as its new director, Bloomberg News reported on Saturday.

The agency, which has been run by acting director Raynard Kington since October 2008 after Elias Zerhouni stepped down, is in late stages of screening Collins, noted Bloomberg.

Fortunately, we can be confident that the rumor isn't true. With Barack Obama as President of the United States, the appointment of someone like Francis Collins should never happen. Things are going to change in Washington.

Wouldn't it be ironic if the rumor were true and the new head of NIH did not have the enthusiastic support of most scientists? That's the sort of thing that happened under the previous President.

Lies, Damn Lies, etc

Thomas Baekdal advises his clients on how to communicate in the 21st Century. He has posted an analysis of current sources of information and his predictions for the future on his blog baekdal.com: Market of Information: Where Is Everybody?.

Here's the graph that everyone's raving about ...

According to Thomas Baekdal, our society is already getting almost 75% of its information from the internet. By 2020 it will be 90%, according to Baekdal.

The surprising thing about this nonsense is the number of people who believe it.¹ The Web 2.0 cult and its various sects have grown into a kind of social movement populated mainly by people under thirty years old, as far as I can tell. These people are predicting that the world will be radically changed in just a few years as newspapers, books, television, and radio die off. They believe that most citizens will be getting all their information from social networks, social news, blogs and websites.

It's reasonable to ask how such predictions are made and, to their credit, some of the people commenting on baekdal.com have asked. Tom Baekdal replies in comment #30.

The graph was based on combination of a lot of things, a number of interviews, general study, general trend movements, my experience etc. I cannot give you a specific source though, because I used none specifically.

The graphs before 1990 are all based on interviews, and a large number of Google searches to learn about the history of Newspaper, TV and Radio - and more specifically, what people uses in the past. The graphs from 1998 and up to today, is based on all the things that have happened in the past 11 years, of which I have probably seen 1000 surveys ( it is what I do for a living). And the graph from 2009 and forward is based on what I, and many other people predict will happen in the years to come.

One very important thing though, this is not a reflection of my opinion. This is the result a careful analysis. There are always variations, and different types of people. But I believe that this graph accurately reflects consumer focus.

That's it folks. This "careful analysis" is what he does for a living and it is NOT just a reflection of his personal opinion.

It sounds to me a lot like the Oprah Winfrey sort of reasoning that we all respect so highly (not!). This is a dangerous trend. What we're seeing here is the abandonment of rational thought in favor of personal experience, wishful thinking, and pseudo-intellectual, scientific-looking analyses.

Nobody doubts that the internet plays an important role in the lives of many people—this is a blog, after all, and it's really, really important.

Nobody doubts that the internet will take up a larger percentage of people's time in the future. But the change will be incremental and supplemental, just as radio, television, email, and cell phones, became part of our lives without transforming them. Newspapers, magazines, and books did not disappear when every home acquired a radio in the 1930s or a television set in the 1960s and they won't disappear when every home has a personal computer.

I tell by students to look at those big boxes hanging from the ceiling in their classroom. They're from 1969 when everyone predicted that television would take over the classroom. My building was even designed with a television studio on the main floor. It's now offices for research administration.

If it's true that in a few short years we will get 90% of our information from the internet then we need to be afraid, very afraid.

The business world will adapt to incremental changes in the way we communicate and gather information. But the proper response is to base business decisions on real scientific analysis of current trends and behaviors and not on the wishful thinking of someone who makes a living by promoting the death of traditional media.

One of the advantages of being an old foggy is that I've lived through several cycles of so-called "futurists" who are convinced they are the prophets of change (e.g. Alvin Toffler, author of Future Shock, 1970; and George Gilder, co-founder of the Discovery Institute). It gets a bit boring after the first fifty years.

1. That means you, Bertalan Meskó of ScienceRoll

Tuesday, May 26, 2009

Happy Towel Day!

Yesterday was Towel Day in honor of Douglas Adams.

The photograph is from the streets of Innsbruck, Austria, in 2005. That's where Adams got the idea to write The Hitchhiker's Guide to the Galaxy.

He hoped and prayed that there wasn't an afterlife. Then he realized there was a contradiction involved here and merely hoped that there wasn't an afterlife.
Douglas Adams

Monday's Molecule #123: Winners

UPDATE: The "molecule" is a normal electrocardiograph (ECG) of a human heartbeat [see Wikipedia: Electrocardiography]. The Nobel Laureate is Willem Einthoven.

There were eight responses in the first hour. The winner is Òscar Reig of Barcelona! This is our first European winner in many months. I guess I'll have to start posting Monday's Molecule much earlier in the day to give Europe a chance. (Australia doesn't get a chance.)

The undergraduate winner is Maria Altshuler of the University of Toronto who just became eligible after winning last month. Congratulations to Òscar and Maria.

This week there were four Europeans and one South American in the hunt. Not only do my Canadian friends need to be worried, but the Americans are also being challenged! I even had a correct entry from Singapore. That presents a real challenge when I try to calculate the winning time. Why can't they use the same day we use?

You've probably noticed already that today's "molecule" isn't exactly a molecule. That's OK, you can still try to guess what it is. I want a fairly complete description of what you see here. This is supposed to be easy in order to encourage some new readers to enter the contest. There was no winner last week!!!

There's a Nobel Prize associated with this diagram.

The first person to describe the graph and identify the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are five ineligible candidates for this week's reward: Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Americans have pulled ahead of the Canadians and the rest of the world is being shut out. Where are the Europeans? Are they just stupid or don't any of them stay up late? BTW, I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

Denyse Hears Lawrence Krauss

Denyse O'Leary is in Sudbury attending the Canadian Science Writers Conference. One of the speakers was Lawrence Krauss&mdahs;who is speaking in Toronto tomorrow evening.

Here's how Denyse reports on what she heard [Science writing: There are not - repeat, NOT - two sides to the story].

Dr. Krauss went on to say that there is an innate tension between journalism and science. The problem is, “journalists think there are two sides to every story.” According to him, this is not true: “Most times, one side is simply wrong.”

Oh well, that’s all right then. Having been informed that one side is simply wrong, the journalist can forget about getting a range of opinion and simply act as a shill for the approved view.

The beauty of that strategy is that if there are problems with the approved view, the journalist is guaranteed never to find out, so she will always be sure she and her sources are right.

Dr. Krauss later conceded that “The editors are the bad guys.” Yes, indeed, in the sense that editors often come up with additional people for us writers to interview, people who offer additional perspectives. They, like us, see most stories as having many sides, not just one, so they are guilty of multiple sins, and we are complicit (when we are doing our job, that is).

The problem with Denyse O'Leary is that she hears but doesn't listen. Krauss said that "most times, one side is simply wrong." He also said that journalists and editors don't get this, they almost always pretend that there are two sides to every story.

Denyse then proves his point.

Brian Switek on the Darwinius Affair

Brian Switek is an undergraduate at Rutgers University in New Jersey (USA). He's the man behind Laelaps.

Brian knows a lot about fossils and the history of life so it's no surprise that he has an opinion about "Ida" the new fossil primate being hyped in the media. Read his article in The Times of London (UK): The dangerous link between science and hype. Brian covers all the bases from whether the science is correct to whether the media hype is justified.

Brian calls himself a science writer and that's a good choice. This is science writing at its very best.

[Photo Credit: Laelaps]

The Perfect Gift

We've all had this problem. Try to choose the perfect gift for your partner without asking their opinion. Chances are, you got yourself in hot water—especially if you're a man choosing for a woman. I still remember¹ buying that cool flash attachment for her 21st birthday ....

It should come as no great surprise that sociologists have studied this phenomenon. Dave Munger at Cognitive Daily has all the details: Why my mom didn't buy me a slot car track for Christmas in 1978, even though I told her that's what I wanted.

The good news is that we aren't alone. The even better news is that women aren't any better at choosing the perfect gift for a man. (It's just that they're less likely to hear about it!)

We've solved the problem in our family. Now we just ask the gift recipient what they want. Last week I got a new GPS system for my car—it was exactly what I wanted for my birthday. How did she know?

1. Because I'm not allowed to forget it!

[Image Credit: How to Choose the Perfect Personalized Sister Gift]

Monday, May 25, 2009

The Fallacy of the Continuum

I once wrote an essay called "Theistic Evolution: The Fallacy of the Middle Ground." The point I was trying to make is that Theistic Evolution does not occupy the middle ground between superstition and rationalism or between science and religion. Theistic evolution is religious, it advocates superstition over rationalism—albeit a milder form of superstition than that of Young Earth Creationists.

Joshua Rosenau supports the evolution/creationism continuum shown in the above diagram [see Creation/evolution continuum, or NCSE is too nice to theists … and to atheists!]. It's from the NCSE website [The Creation/Evolution Continuum].

Josh claims that the continuum is the proper way to illustrate the differences between those who accept evolution and those who don't.

The nice thing about the continuum graphic is that, regardless of its faults, it emphasizes an easily obscured point: one need not set evolution against belief in a deity who acts in the world, and it is possible to move toward acceptance of evolution without moving out of the realm of theistic belief. The continuum oversimplifies by making it seem like there's just one path one might take in doing so, but NCSE is not in the business of endorsing particular religious philosophies, and making an exhaustive list is beyond the scope of the continuum.

He's got one thing right. It is, indeed, possible to move toward rationalism and science without moving out of the realm of theism. What Josh doesn't understand is that there's a breakpoint not shown on the continuum. I've put it on the modified version I show here.

When you view it like this, it's a different sort of diagram. There is a sort of continuum as theists move farther and farther away from the most outrageous forms of anti-science belief. But there's no continuum between science and most forms of religious belief. That's a sharp line.

Is there a reason for spinning the debate in the form of a continuum? Yes, there is ... you've heard it before.

More significantly, the continuum is helpful as a way to reach out to folks who have simply never thought about the issue before, and naively assume there are two camps: one for creationism and the other for evolution. So when forced to choose (as, for instance, by a pollster) they glom onto whichever camp they think best fits them. If the question is asked in a way that frames the decision in terms of science, they'll tend to favor evolution, if framed around religion or morality, they tend to choose creationism (at least in the US). Pointing out that there is a broad and diverse middle ground, that the choice is not nearly so stark, can help people get comfortable accepting evolution before confronting religious issues.

I understand why framing the debate in this way can be helpful to your cause. What I object to is the implication that moving from theism to atheism via agnosticism is a smooth transition. That's just not true and NCSE is very much endorsing a certain philosophical position when it promotes this diagram.

The continuum is a tool, and a useful one. It helps introduce the complexities of the interplay between science and religion to audiences who may simply think that everyone has to choose one or the other. It often surprises audiences to learn that many people do not see a need to choose, do not find an inherent conflict. (Standard disclaimer/troll repellent: Those people might be wrong, and I take no position on that topic.)

No, Josh, that's not true. You are taking a position on that topic. You are saying that one does not have to choose one or the other. You are saying that the view of evolution espoused by Francis Collins differs only in subtle degrees from that espoused by atheist scientists. You must know that isn't true.

As such, the simple tactic of drawing a bridge between what people think of as two mutually exclusive beliefs is pedagogically powerful.

There is no "bridge" between the belief in supernatural being and non-belief in such beings. How can something be "pedagogically powerful" if it's wrong?

An Ethical Question

Eva Amsen was reading a book in a student study lounge when she was asked to participate in a survey [Spent - Review]. The question was ....

It was a short questionnaire about what you would do if you were standing in line at the post office for more than 30 minutes, waiting to mail a package, and someone offered to take you to the front of the line in exchange for $3. Would you pay the three dollars or keep waiting?

My answer is different than Eva's so this got me thinking.

See the poll in the left sidebar. What would you answer?

Is there a "right" answer?

Monday's Molecule #123

You've probably noticed already that today's "molecule" isn't exactly a molecule. That's OK, you can still try to guess what it is. I want a fairly complete description of what you see here. This is supposed to be easy in order to encourage some new readers to enter the contest. There was no winner last week!!!

There's a Nobel Prize associated with this diagram.

The first person to describe the graph and identify the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are five ineligible candidates for this week's reward: Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Americans have pulled ahead of the Canadians and the rest of the world is being shut out. Where are the Europeans? Are they just stupid or don't any of them stay up late? BTW, I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

The Darwinius Affair Continues to Embarrass

Today's the day we get to see the global event of the century, or is it millennium?. Sometime this evening there will be a TV show on one of the cable channels. It will reveal the astonishing fossil find that proves once and for all that humans have evolved. (Or something like that.)

The Darwinius Affair continues to embarrass everyone, including the creationists.

A friend alerted me to an article in The Bapstist Press (don't ask): Experts: Fossil find exciting but lacks significance . The article quotes certain "experts" including Kurt Wise the creationist who was a graduate student of Stephen Jay Gould.

"It is always exciting to find a well-preserved fossil, especially of something as rarely preserved as a juvenile primate," Wise wrote in a statement to Baptist Press. "The Messel site has generated a large number of spectacular fossils. Although the sediments seem to have been from a lake, it is an unusual one, somehow allowing remarkable preservation of animals both of the lake and the land.

"The unusual conditions of the Messel lake were probably created by a combination of global warmth (a much warmer earth than that of the present day) and the presence of active supervolcanoes (much larger than any known today) -- both a consequence (I believe) of the earth recovering from the effects of Noah's Flood," Wise, professor of science and theology and director of the Center for Science and Theology at Southern Baptist Theological Seminary, said.

There's more than enough embarrassment to go around, however, evolutionists should take heed when Answers in Genesis (AiG) says ....

The group also said the pitch of Ida as the missing link is "full-out sensationalism by people who are bypassing the scientific community with a direct-to-the-public appeal on behalf of Darwinism."

"All of this seems a departure from the normal turn of events, where researchers study their subject and publish their findings, and let the media chips fall where they may," AiG said.

I agree with Answers in Genesis.¹ We handed this to them on a golden platter and they are right to make it into a big deal. Shame, shame on all the scientists and media types who turned this minor, but interesting, discovery into a public-relations disaster.

1. Whew! I never thought I'd say that.

Franzen, J.L., Gingerich, P.D., Habersetzer, J., Hurum, J.H., von Koenigswald, W., et al. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. [doi:10.1371/journal.pone.0005723]

Saturday, May 23, 2009

I'm really, really hoping this is a joke.

Friday, May 22, 2009

No Democrats Allowed at Liberty University

Liberty University has shut down the students Democrats club. You can read all about it on Pharyngula [“Liberty” University really ought to look at the first word in their name].

The email message has been published by the Washington Post. It needs to be widely circulated to illustrate just how Liberty University is treating its students.

From: Hine, Mark (VP Student Affairs)
Sent: Friday, May 15, 2009 1:37 PM
Subject: LU College Democrats

I must inform you that the College democrats' club is no longer going to be recognized as a Liberty University club. We are unable to lend support to a club whose parent organization stands against the moral principles held by Liberty University. I expressed these concerns when we met, earlier in the spring semester.

The Liberty Way states, "It is the duty of every student to respect Liberty's Statement of Doctrine and Purpose. They may not engage in any activity on or off campus that would compromise the testimony or reputation of the University or cause disruption to Liberty's Christian learning environment."

The Liberty University School of Law had been working on a policy to govern their clubs and organizations for quite some time. They have now completed that policy and we have adopted it for Liberty University as well. Now that it has been adopted and will apply to all clubs and organizations, it is clear that this club does not comply.

Below is a copy of the policy which governs clubs and organizations at Liberty University. This policy is posted on the website.
STUDENT CLUBS AND ORGANIZATIONS POLICIES

Student clubs or organizations must request and receive permission from the Liberty University administration before they may meet on campus, advertise, distribute or post materials, or use any University facilities for their activities or events. All such clubs or organizations and their activities or events must be consistent with the University's mission, and must be and remain in compliance with the Liberty Way, the Honor Code, and any policies or procedures promulgated by the University. The University reserves the right to refuse the use of its facilities for any reason to any student club, organization, activity or event.

Consistent with the Honor Code, all students, student clubs and organizations, faculty and staff of Liberty University, have a responsibility to uphold the moral and ethical standards of this institution and personally confront those who do not.

No student club or organization shall be approved, recognized or permitted to meet on campus, advertise, distribute or post materials, or use University facilities if the statements, positions, doctrines, policies, constitutions, bylaws, platforms, activities or events of such club or organization, its parent, affiliate, chapter or similarly named group (even if the similarly named group is not the actual parent, affiliate or chapter) are inconsistent or in conflict with the distinctly Christian mission of the University, the Liberty Way, the Honor Code, or the policies and procedures promulgated by the University.
Even though this club may not support the more radical planks of the democratic party, the democratic party is still the parent organization of the club on campus. The Democratic Party Platform is contrary to the mission of LU and to Christian doctrine (supports abortion, federal funding of abortion, advocates repeal of the federal Defense of Marriage Act, promotes the "LGBT" agenda, Hate Crimes, which include sexual orientation and gender identity, socialism, etc). The candidates this club supports uphold the Platform and implement it. The candidates supported are directly contrary to the mission of LU. By using LU or Liberty University and Democrat in the name, the two are associated and the goals of both run in opposite directions.

We are removing the club from the Liberty website and you will need to cease using Liberty University's name, including any logo, seal or mark of Liberty University. They are not to be used in any of your publications, electronic or internet, including but not limited to, any website, Facebook, Twitter or any other such publication.

If you have questions please do not hesitate to contact me.

Mark Hine
VP for Student Affairs
Liberty University

This is just the beginning. Mark my words. In a few weeks they're going to shut down the "Liberty University Gays and Lesbians Club" and the "Liberty University Secular Humanist Club." And it's only a matter of time before the "Liberty University Teletubbies Fan Club" is kicked off campus.

Teaching Evolution in Natural History Museums

In an article published last November in Trends in Ecology & Evolution, Bruce MacFadden urges that natural history museums explore the use of new displays, such as those involving genomics and molecular biology, to educate the general public [Evolution, museums and society].

He writes ...

Public understanding of evolution has changed little over the past quarter-century [4]. The challenge therefore remains for natural history museums to improve communication about evolution, particularly the more difficult concepts.

MacFadden notes that museum visitors are more likely to accept evolution. Museums need to do a better job of taking advantage of this fact in order to enhance understanding of evolution.

Evolution represents a complex array of concepts, some of which are well understood whereas others are poorly understood by museum visitors. If an institution is committed to improving public understanding about evolution, then additional resources and effort should be directed toward more effectively communicating the more poorly understood concepts such as natural selection.

Yes, natural selection is difficult but random genetic drift is even more difficult. Unfortunately, I don't get the impression that MacFadden is counting random genetic drift as one of the basic concepts that museum visitors need to learn about.

One solution is to create displays about molecular evolution.

In this regard, there is much room to highlight research traditionally not considered to be natural history, such as genomics and molecular biology [9], although these subjects are not usually specimen based and therefore potentially less attractive to the public. In these instances, visitors are more likely to grasp difficult concepts when they have some prior understanding of a topic [10], or can place these concepts in a modern-day societal context. For example, disease vectors such as influenza and malaria mutate rapidly to become drug resistant, and therefore have negative consequences for world health.

This is a good idea. I recently visited the American Natural History Museum in New York and it had an excellent display on molecular evolution. It showed how you could compare DNA sequences and it explained that many of the mutations were just accidents that became fixed in the population by genetic drift. It even mentioned junk DNA and messy genomes.

It was a very popular display. Not only did it highlight some of the most important evidence for the history of life, it also explained the two main mechanisms of evolution. There were more people reading the material in the molecular evolution area than in the more traditional fossil areas. DNA is exciting.

Kotiaho et al. (2009) disagree. In the June issue of Trends in Ecology & Evolution they write [Evolution education in natural history museums ] ...

In his essay, MacFadden advocates the allocation of resources into novel contents, such as genomics or molecular biology, in order to increase the public understanding of evolution. We argue that museums should concentrate more on demonstrating the basic principles and outcomes of natural selection, rather than presenting fashionable novel contents such as genomics (which, it seems, even scientists often have a hard time understanding [4]).

It's clear that Kotaiho et al. see natural selection as the main (only?) mechanism of evolution. What they want is the kind of display that illustrates natural selection. They like dioramas.

If we want to educate the visitors of natural history museums about evolution by means of natural selection, we should aim at delivering the message that across species there is enormous within-species variation, that some of this variation is likely to cause differences among individuals in their lifetime reproductive success and that these differences will result in a constant change – evolution. In museums, we have a great opportunity to do this; as well as the exhibits open to the public, museums usually have extensive collections containing numerous individuals of each species. A simple illustration of the replacement of one generation by the next generation might work in making the operation of natural selection more tangible. With such an illustration, we can easily see why and how a population can undergo constant change, and thus grasp the basic principles of evolution by means of natural selection.

Natural history museums are our collective memory of the past. Their collections can, and have been, used to study evolution (e.g. [7]). Perhaps even more importantly, however, they could also be used to illustrate to the general public the evolutionary changes that have taken place. We challenge the exhibit designers of natural history museums to emphasize variation within species, and to demonstrate change due to natural selection, rather than stasis in nature.

Here's the problem. It might be fine to mount a display showing variation within a population. It might be possible to construct a display where the next generation has a different degree of variation. But it would be wrong to attribute that to natural selection unless you could present evidence that there were fitness differences associated with those variants.

I fear that these authors are not distinguishing between evolution and natural selection. They think that evidence of evolution is evidence of natural selection.

I don't understand why Kotaiho et al. would want to ignore molecular evolution and genomics. There's no better way to illustrate random genetic drift and there's no excuse for eliminating one of the most important fields in modern evolutionary biology.

Thursday, May 21, 2009

The Darwinius Affair

The Darwinius Affair is getting messier. Not only did some scientists commit a serious breach of scientific ethics by exaggerating their claims about the fossil, but they also prevented legitimate science journalists from doing their job.

As most of you know, I think that science journalists should examine the claims of scientists in order to ensure they are accurate. They should not just take the word of the scientist, no matter how famous he or she is.¹

In order to do their job, the science journalists need access to the scientific paper before it is released to the public. This is standard practice. Journalists are used to, and respect, news embargos.

In this particular case, it appears that scientists and the editors of PLoS ONE prevented journalists from seeing the paper until the press conference and all the associated hoopla was under way. Carl Zimmer has the story at Science Held Hostage.

Shame on PloS ONE, on the scientists who wrote the paper, and on everyone else who is associated with this media event. This is not how science is supposed to work. This is not how we should be communicating with the general public.

Franzen, J.L., Gingerich, P.D., Habersetzer, J., Hurum, J.H., von Koenigswald, W., et al. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. [doi:10.1371/journal.pone.0005723]

1. Most professional science journalists don't do this, but that's another issue.

Wednesday, May 20, 2009

It's that time of year, again.

The course is over, the exam has been written, the marking is done, and the grades have been submitted. There's a short lag while the marks are checked and then they're posted so that students can learn how they've done in the course.

At my university we submit grades as percentages. They are converted to grade points (out of 4) in order to calculate a grade point average. The percent score is reported on the transcript and so is the grade point average. ~~A mark of 76% is a 3.0, a mark of 77% is a 3.5 and a mark of 80% is a 3.7.~~ A mark of 76% is a 3.0, a mark of 77%-84% is a 3.7, and a mark of 85% or above is a 4.0. There is no 3.5—shows you how much attention I pay to those sorts of things.

The email messages start as soon as the marks are posted. Every year there are students who want more marks. Usually it's just a few more marks to raise their grade points from 3.3 to 3.7 or something similar. That's by far the most common request. Sometimes the student wants lots more marks because they worked really hard in the course and deserve a much higher grade.

The most common reasons for asking for more marks are ...

losing a scholarship
not going to get into medical school/graduate school
grade doesn't reflect effort
parents will be disappointed
the final exam was unfair
student wasn't feeling well during the test that gave the lowest score
this is the lowest grade ever received

Some of the letters just ask me to give them more marks because I feel sorry for them. But many contain the suggestion that they are willing to pay for a higher grade. Fortunately, I can handle all these requests by just referring students to the standard appeal process. Once the grades are submitted to the Faculty I can't change them. It's one of the few times that I like the rules and regulations.

Every Professor in the Department gets these requests at this time of the year.

Here's the important part—it's not fair to put the entire blame on the students. There's something about the way we run the university that makes it seem acceptable to beg for higher marks. What are we doing wrong? How can we fix it?

I have a trivial solution that will deal with many of the problems.

ABOLISH GRADE POINTS AND GRADE POINT AVERAGES

Nobel Laureate: Charles Robert Richet

The Nobel Prize in Physiology or Medicine 1913

"in recognition of his work on anaphylaxis"

Charles Robert Richet (1850 - 1935) won the Noble Prize in 1913 for discovering the phenomenon known as anaphylaxis. This is a condition where the administration of an antigen causes severe symptoms, even death. Richet found that anaphylactic shock occurs only after an animal had been previously immunized and even then only after some days had passed.

It appeared as though the first immunization took several days to develop but when the process was complete a second attempt at boosting immunization causes a severe reaction. Anaphylactic shock was rare, it only happens in a small percentage of cases. We are familiar with the risk when people are known to be allergic to peanuts or insect stings.

Today we know what causes the symptoms of anaphylaxis; it's due to massive release of histamines, prostaglandins, and leukotrienes from mast cells. The release of these chemicals produces rapid heartbeat, sweating, and constriction of the airways. The symptoms can be relieved, and death prevented, by rapid treatment with epinephrine.

The primary cause of most anaphyaxis is overproduction of antigen-specific immunoglobulin E (IgE) molecules on the mast cells.¹ It's the IgE molecules that interact with the antigen to cause release of histamines etc. It's not known why some antigens lead to overproduction of IgE such that subsequent exposure to the same antigen cause a massive allergic reaction. (Normal antibodies are immunoglobulin G or IgG.²)

Immunology is complicated. That's why we can't cure asthma and other allergic reactions even though the phenomena have been intensely studied for more than 100 years.

Here's an excerpt from the 1913 Presentation Speech.
THEME:
Nobel Laureates

In an age in which the leading members of the medical profession tend to concentrate on innumerable experiments demonstrating the growing immunity of the organism towards poisons already resisted successfully once, you, Sir, have found that in certain cases a completely opposite result is produced. You did not restrict yourself to this isolated observation: studied in depth by you, it has become the foundation on which you have based the evidence of a reaction that is sometimes just as regular as the phenomenon of immunity. We are not concerned solely with specific prophylaxis; thanks to you, we are now aware of a specific anaphylaxis.

We do not discount the work of those who, following your lead, have observed similar phenomena, but to you goes the honour of having established the basis of a new biological reaction, anaphylaxis, and of having been the first to demonstrate it clearly. Thereby you have opened up to medical science an enormous field of study as yet unexplored. The Staff of Professors of the Caroline Institute wishes to reward you for this achievement by conferring on you the prize instituted by our compatriot Alfred Nobel for those «who have made the most important discovery in the field of physiology or medicine».

Please accept the warm congratulations of the Institute and myself, together with the wish of us all that success will continue to crown your devoted work.

1. I do not mean to imply that IgE molecules are produced by mast cells. They are not.

2. There are several different classes (isotypes) of antibodies; IgG, IgD, IgM, IgA, and IgE. The most abundance class is IgG—that's the one most often depicted in the textbooks. It's probably the type most people think about when they think about antibodies. I did not mean to imply that the other classes are not "normal."

[Photo Credit: Wikipedia]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Science Journalism at its Worst

This video is an embarrassment. At a time when we are trying to convince the public that science is credible, along comes a trashy exploitation that sets science back several decades.

This is not how science works. It is not accurate science and it is not an accurate depiction of how scientists will react to the discovery of Darwinius masillae.

Cafe Inquiry: Freedom of Speech and the Atheist Bus Campaign

Join us on Friday night for a discussion about Freedom of Speech and the Atheist Bus Campaign.

Modeled on the highly popular Cafe Scientifique, Centre for Inquiry presents Cafe Inquiry. Join us for a series of interactive forums exploring contemporary issues in science, reason, philosophy and politics. We bring you 2 or 3 guest experts that open by addressing the issue from a variety of perspectives and responding to moderator questions. Then we open it to the floor for your questions and comments to the panel and each other. This is your chance to interact with a diverse group of people on CFI's broad topics.

I've met some of the people who were involved in the atheist bus campaign. This promises to be a fun evening. If you've never been to an event at the Centre for Inquiry you can get in touch with me. I'll be happy to meet up with you and take you to the location.

What Fools Those Atheists Be!

Read Lord! What Fools Those Atheists Be! in Report Magazine. (Report Magazine is published in Edmonton, ~~Texas~~ Alberta. It bills itself as "Western Canada's Conservative Voice.") The author of the offensive article is Pastor Shafer Parker, a Texas native who is now with the Hawkwood Baptist Church in Calgary.

Before you read the article, answer the poll question in the left-hand sidebar: "Do you believe that there is a 'God'"? So far, the answer "Absolutely!" is leading over "Absolutely Not!" but it's early days.

Heathen Mike of Mike's Weekly Skeptic Rant has dissected most of the article at: Shafer Parker, Answered. You should read what Mike has to say. I'm sure you'll be convinced that it's not the atheists who are the fools.

Most of Pastor Parker's rant is against the bus ads promoting atheism. I want to address one particular point in Parker's article. He says ...

The Christian West's centuries-old tradition of free expression and open debate is unique in that nothing like it exists anywhere else on earth. No such tradition exists in any society dominated by a single non-Christian faith, including the atheistical Communist-materialist nations of China, North Korea and the former Soviet Union. It is not an accident that these ads have deliberately set out to offend the majority Christian theists living in London, Madrid and Washington, D.C. They would not have been allowed in Beijing, New Delhi or Riyadh.

Parker believes that Christianity is associated with free expression and open debate. He claims that no other religion has a similar tradition. This would have been news to the people of Cordova in the Moorish Kingdom from 800-1200 AD. It would also have been news to most Catholics throughout history and to most Protestant sects (e.g. Puritans). They aren't exactly noted for tolerating free expression and open debate. (Were the ancient Greeks Christians?)

But let's put history aside. It's obviously not one of Parker's strong points. Let's just look at Christian nations in the last century or so. Mussolini's Italy and Franco's Spain come to mind. So does Czarist Russia. I'm sure there are plenty of other Christian nations where free expression and open debate were not common—I'm thinking of several nations in Central and South America. I don't think he's making a valid point. I don't think the concept of free expression is in any way a product of Christianity.

What about modern states? Israel, Japan. and India seem to be non-Christian states that have a certain degree of free expression and open debate. Parker says that the atheist signs would not be allowed on buses in New Delhi. I suspect he's wrong about that. In any case, he ignores the fact that the atheist signs will never be allowed in some of the most Christian parts of America. Isn't that strange?

Tuesday, May 19, 2009

Monday's Molecule #122: Winner?

UPDATE: The molecule is epinephrine or adrenaline. IUPAC name = (R)-4- (1-hydroxy-2- (methylamino)ethyl)benzene-1,2-diol.

The Nobel Laureate is Charles Robert Richet who discovered and described anaphylaxis or anaphylactic shock. Epinephrine, in the form of an EpiPen, is used to treat anaphylactic shock.

Ten people got the molecule but Dima Klenchin was the only person to guess the correct Nobel Laureate. He isn't eligible so there is no winner this week.

Today's molecule is a drug as well as a biological molecule that's found in some species. You need to supply the common name and the correct IUPAC name for this molecule. The stereochemistry isn't shown in the figure but you have to specify it in your answer.

As a drug, this molecule is used to treat a common but life-threatening condition. Identify that condition and name the Nobel Laureate who first described and characterized it.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Canadians are still ahead in the competition between Canadians the rest of the world but their recent dominance is coming to an end. I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

~~Comments will be blocked for 24 hours.~~ Comments are now open.

Monday, May 18, 2009

Science for Humanity

Today's issue of The Toronto Star has an article on Andras Nagy, a colleague who works at one of the hospital research institutes here in Toronto. Apparently Nagy made a list of "Top 10 awards for work in science-related endeavours" in a magazine called Scientific Magazine [Scientist honoured for stem-cell coup].

I tried to find this magazine and the names of the other winners but nothing seemed to work. Google was not my friend today.

Later on, after lunch, I noticed a press release from "Scientific American." That magazine was naming "Ten researchers, politicians, business executives and philanthropists who have recently demonstrated outstanding commitment to assuring that the benefits of new technologies and knowledge will accrue to humanity" [Scientific American 10: Guiding Science for Humanity].

Sure enough, Andras Nagy was on that list. Here's the complete list. Congratulations to Genie Scott.

Todd Brady
Corporate environmental manager
Intel, Santa Clara, Calif.
A chip company makes expansion of its environmental footprint a priority

Shai Agassi
Founder and chief executive
Better Place, Palo Alto, Calif.
A wonderfully simple recharging scheme may ensure a future for electric vehicles

Wafaa El-Sadr
Chief
Infectious Disease Division, Harlem Hospital Center, New York City
The physician leads a multipronged public health campaign to fight the scourge of HIV

Robert J. Linhardt
Professor of Biocatalysis and Metabolic Engineering
Rensselaer Polytechnic Institute
A chemical sleuth unravels the cause of deaths from a tainted drug

Eugenie Scott
Executive director
National Center for Science Education, Oakland, Calif.
A champion for the teaching of evolution steps up her advocacy

Bill Gates/Michael Bloomberg
Co-chair
Bill and Melinda Gates Foundation
Mayor of New York City
Celebrity heft propels a campaign to limit smoking

Bryan Willson
Professor of mechanical engineering
Colorado State University
An engineer facilitates clean energy technology for the developing world

Kristian Olson
Program Leader
Center for Integration of Medicine and Innovative Technology, Boston
Simple, low-cost resuscitators and incubators can save newborns in the developing world

Andras Nagy
Senior investigator
Mount Sinai Hospital, Toronto
A biologist discovers a practical method of making stem cells from mature cells

Barack Obama
President of the U.S.
The new chief executive begins his term by initiating a radical shift in science policy

It would be fun to see the top ten scientists—men and women who have contributed the most to our understanding of the natural world.

Monday's Molecule #122

Today's molecule is a drug as well as a biological molecule that's found in some species. You need to supply the common name and the correct IUPAC name for this molecule. The stereochemistry isn't shown in the figure but you have to specify it in your answer.

As a drug, this molecule is used to treat a common but life-threatening condition. Identify that condition and name the Nobel Laureate who first described and characterized it.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Canadians are still ahead in the competition between Canadians the rest of the world but their recent dominance is coming to an end. I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

Who Knew?

The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.

Evolution News & ViewsJonathan Wells has a Ph.D. He can explain why "Darwinism" is false in only two paragraphs [Persisting in Spite of the Evidence: Why Darwinism Is False].

Darwin called The Origin of Species “one long argument” for his theory, but Jerry Coyne has given us one long bluff. Why Evolution Is True tries to defend Darwinian evolution by rearranging the fossil record; by misrepresenting the development of vertebrate embryos; by ignoring evidence for the functionality of allegedly vestigial organs and non-coding DNA, then propping up Darwinism with theological arguments about “bad design;” by attributing some biogeographical patterns to convergence due to the supposedly “well-known” processes of natural selection and speciation; and then exaggerating the evidence for selection and speciation to make it seem as though they could accomplish what Darwinism requires of them.

The actual evidence shows that major features of the fossil record are an embarrassment to Darwinian evolution; that early development in vertebrate embryos is more consistent with separate origins than with common ancestry; that non-coding DNA is fully functional, contrary to neo-Darwinian predictions;¹ and that natural selection can accomplish nothing more than artificial selection — which is to say, minor changes within existing species.

Amazing.

When it comes to evaluating Creationist arguments, we are often faced with a difficult decision. Is the Creationist just ignorant or is he lying? I think it's much easier to answer that question in Wells' case. He has a Ph.D. in biology from a reputable university. It's not possible for him to be that ingnorant about the basic facts of biology.

1. It's a lie that non-coding DNA is fully functional and it's a lie that "neo-Darwinism" predicts the presence of large amounts of junk DNA in some species.

One Angry Christian

Charlotte Allen doesn't like atheists very much. She writes in Los Angeles Times [Atheists: No God, no reason, just whining].

I can't stand atheists -- but it's not because they don't believe in God. It's because they're crashing bores.

She then proceeds to describe all the "boring" things that upset her.

I'd like to comment on one of the points that she makes.

The problem with atheists -- and what makes them such excruciating snoozes -- is that few of them are interested in making serious metaphysical or epistemological arguments against God's existence, or in taking on the serious arguments that theologians have made attempting to reconcile, say, God's omniscience with free will or God's goodness with human suffering.

This is becoming a mantra for Christian apologists and it's about time we put an end to it.

The reason why atheists aren't interested in making serious arguments against God's existence is that it's impossible to prove the non-existence of something. On the other hand, we can easily show that the arguments in favor of supernatural beings are nonsensical. There are no "serious mtaphysical or epistemological arguments" for God and that's what we point out to anyone who takes the time to listen.

I suppose that makes us boring.

Furthermore, atheists are not interested in "taking on" the "serious" (sic) arguments of theologians when they attempt to reconcile their God with free will and evil. Why should we be interested in such arguments? The premise behind these arguments is that God exists. Atheists reject the premise. If they want to be taken seriously, "serious" theologians have to first prove that God exists before they begin their apologetics.

Christians like Charlotte Allen make me angry. It's not because they're Christians, it's because they are so irrational.

What atheists don't seem to realize is that even for believers, faith is never easy in this world of injustice, pain and delusion. Even for believers, God exists just beyond the scrim of the senses. So, atheists, how about losing the tired sarcasm and boring self-pity and engaging believers seriously?

OK. Here's an attempt to engage believers seriously.

If believing is so hard in the face of the real world, and if your belief is "just beyond the ... senses," then why do you continue to believe?

[Hat Tip: RichardDawkins.net]

Happy Victoria Day!

Today's the day we celebrate Queen Victoria's birthday (Victoria Day) in most Canadian provinces. Queen Victoria was actually born on May 24th but the modern holiday is the first Monday before or on May 24th.

Since the death of Queen Victoria, the holiday does double duty as a celebration of the birthday of the current monarch. Queen Elizabeth II was actually born on April 21st—it must be nice to have two birthday parties every year!

Although Queen Elizabeth II is officially Canada's head of state, the duties are actually carried out by her representative, the Governor General. Governors General are appointed every few years and their duties are largely ceremonial. I really like a system where the head of state is not the same person as the head of government. It avoids a lot of problems.

Officially, Canada's form of government is called a Constitutional Monarchy with a Parliamentary System of government.

[The painting of Queen Victoria's Family in 1846 is by Franz Xaver Winterhalter.]

Saturday, May 16, 2009

Michael Bliss - Anti-Science Conservative

Michael Bliss is a Professor Emeritus at the University of Toronto. He has written some excellent books on the history of science, notably a book about the discovery of insulin.

Bliss has always been a small-c conservative and many of his opinion pieces have supported conservative policies.

On Thursday, May 14th, Michael Bliss entered the debate on Canadian science funding [Michael Bliss: Anti-Harper campaign politicizes research to the detriment of science]. His main point is that Canadian scientists are whiners and complainers who should keep their mouths shut because they are damaging the reputation of science in Canada.

It’s time that responsible leaders of the Canadian science and research communities began thinking of ways to cool down their more hot-headed colleagues. The strategy of declaring war on a government because some of its policies are temporarily inconvenient and vexatious can generate cheap short-term applause and support in some quarters, but in the long run tags its adherents as unreliable and unworthy, or worse. Eventually doors get shut in their faces, and/or they’re left to wither on the vine.

It’s a sad way to tarnish what often has been and still could be one of the success stories of Canadian public policy.

I've never been a fan of Michael Bliss but this diatribe goes way over the line. Scientists are justifiably criticizing a science policy that they feel is doing great damage to Canada's ability to be competitive in the 21st century. Michael Bliss is saying that scientists should not speak out when they disagree with government policy. That's a strange position for someone who has made a reputation of speaking out on controversial topics.

But it's at least consistent with conservative thinking.

Michael Bliss thinks it's OK for governments to direct scientific research. He thinks the only important kind of research is that which directly benefits business and consumers. Applied research and technology is "accountable."

By and large, Canadian researchers have not had a bad inning in recent years. Some observers think that the research community has actually had an easy ride, never having been forced to show exactly what benefits are being generated for the Canadian people by the money given researchers. If the government of Canada ever decided, for example, that this country should lead the world in demanding hard accountability from researchers who live off taxpayers’ largesse, today’s discontents would seem like extremely small beer.

I suppose that's why Bliss admires Banting and Best and the others who discovered and produced insulin. I suppose he hates those scientists who discovered recombinant DNA technology to help with their curiosity motivated research even though it led directly to the production of human insulin—a far more effective form than the old insulin from pigs.

The main product of research is knowledge and knowledge is always of more benefit to the Canadian people than ignorance. During his many decades at the University of Toronto, Michael Bliss and his students contributed to that knowledge base in many ways. Some of the work in history that he published was paid for by research grants. I wonder if he can meet the demand of "hard accountability" that he demands of others? With respect to his own scholarly work, I wonder if he can explain "exactly what benefits are being generated for the Canadian people"?

(Read Commentary strives to politicize science funding debate on Researcher Forum for a similar perspective on Michael Bliss.)

Stephen Harper: Just Leaving

Godless Radio

Yesterday I was interviewed on Godless Radio by Godless Dave and Godless Rob. It was a fun time. We spent an hour talking about the conflict between science and religion. I think we pretty much solved all the problems.

There will be a podcast version for those of who missed the live broadcast.

Godless is an internet radio show designed to give atheists at the University of Toronto, Scarborough Campus, a voice. We aim to reach out to non-believers, whether they call themselves atheists, agnostics, secular humanists or anything else, and provide a platform for the promotion of reality-based thinking.

Friday, May 15, 2009

Metabolism First and the Origin of Life

There are several competing hypotheses about the origin of life. Most people know about the Primordial Soup scenario; that's the one where complex organic molecules are created by spontaneous chemical reactions. Over time these complex molecules, such as amino acids and nucleotides, accumulate in a warm little pond and eventually they come together to form proteins and nucleic acids.

The RNA World scenario is similar except that nucleic acids (RNA) are thought to form before proteins. For a while, RNA molecules are the main catalysts in the primordial soup. Later on, proteins take over some of the catalytic roles. One of the problems with the RNA world hypothesis is that you have to have a reasonable concentration of nucleotides before the process can begin.

The third hypothesis is called Metabolism First. In this scheme, the first reactions involve spontaneous formation of simple molecules such as acetate, a two-carbon compound formed from carbon dioxide and water. Pathways leading to the synthesis of simple organic molecules might be promoted by natural catalysts such as minerals and porous surfaces in rocks. The point is that the origin of life is triggered by the accumulation of very simple organic molecules in thermodynamically favorable circumstances.

Simple organic molecules can then be combined in various ways that result in simple amino acids, lipids, etc. These, in turn, could act as catalysts for the formation of more organic molecules. This is the beginning of metabolism.

Eventually simple peptides will be formed and this could lead to better catalysts. Nucleic acids and complex amino acids will only form near the end of this process.

One of the advantages of the metabolism first scenario is that it offers a simple "solution" to the chirality/racemization problem by explaining why all naturally occurring amino acids are left-handed [see Can watery asteroids explain why life is 'left-handed'?]. Another advantage is that it doesn't require spontaneous formation of nucleotides—a major limitation of the RNA world scenario since spontaneous formation of such molecules is very improbable.¹

James Trefil, Harold Morowitz, and Eric Smith have written up a very nice summary of the Metabolism First hypothesis for American Scientist: The Origin of Life. The subtitle, "A case is made for the descent of electrons," is a clever play on words. It illustrates the point that synthesis of simple organic molecules such as acetate are thermodynamically favorable. This is science writing at its best.²

The authors have reconstructed the simplest, most fundamental, biochemical pathways concluding that a reductive citric acid cycle is probably the best example of the first metabolic pathway. In this pathway, the two-carbon acetate molecule is made from carbon dioxide and water in the reverse of the common citric acid pathway found in eukaryotes.

In fact, the reductive pathway occurs in many bacteria. They can still use it to fix carbon. The authors use the figure on the left to illustrate the basic pathway.

Almost all of the common molecules of life are synthesized from acetate or the molecules of the citric acid cycle. The simple amino acids, for example, are formed in one step. More complex amino acids are derived from the simple amino acids, etc. Similarly, simple fatty acids can be formed from acetate and more complex ones come later; once the simple ones accumulate.

The central role of citric acid cycle metabolism in biochemistry has been known for decades. It's involvement in biosynthesis pathways is often ignored in introductory biochemistry courses because they are heavily focused on fuel metabolism in mammals and biosynthetic pathways get short shrift in such courses.

The essence of Metabolism First is that the various complex molecules of life came after the spontaneous formation of very simple molecules. Pathways leading to the complex molecules evolved and their evolution was assisted by the evolution of various catalysts, some of which were biological in nature.

1. In spite of the claims surrounding a recent paper in Nature: RNA world easier to make.

2. Probably good science editing as well. My friend Morgan Ryan is managing editor and he is very good.

[Photo Credit: American Scientist, courtesy of Scripps Institution of Oceanography, University of California, San Diego.]

Get a Job in Waterloo

Biology - Assistant Professor (Invertebrate Developmental Biology)
University of Waterloo
Location: Ontario
Date posted: 2009-04-06

Invertebrate Developmental Biologist.

The Department of Biology of the University of Waterloo invites applications for a tenure track position at the assistant professor level in invertebrate developmental biology. Applicants must have a PhD and be prepared to establish an active research program; evidence of the ability to attract independent research funding and/or teaching experience would be an asset. We are particularly interested in applicants using genetic approaches to model invertebrate systems in conjunction with modern imaging techniques. Duties include research, management of departmental imaging facility, teaching at the undergraduate and graduate levels, as well as graduate student supervision.

Applicants should send their curriculum vitae, the names of three references and an outline (one to two pages) of their proposed research program, by electronic means if possible, to: D.R. Rose, Chair, Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1 Canada, or via email to givan@sciborg.uwaterloo.ca.

The closing date for applications is May 15, 2009 with a start date no later than September 1, 2009.

All qualified candidates are encouraged to apply; however Canadian and permanent residents will be given priority. The University of Waterloo encourages applications from all qualified individuals, including women, members of visible minorities, native peoples, and persons with disabilities. This appointment is subject to availability of funds. Additional information on the Department is available at http://www.biology.uwaterloo.ca/.

Thursday, May 14, 2009

The Problems with Research Funding in Canada

Jim Turk is Executive Director of the Canadian Association of University Teachers (CAUT). He is a staunch defender of university research, especially curiosity motivated research.

In Tuesday's Globe and Mail, Turk explains why current government policy is wrong. It puts too much emphasis on research that directly helps business and not enough on fundamental research [Get the state out of the labs of the nation].

He also makes a point that needs emphasis. The Presidents of Canada's granting agencies are getting into bed with the government. They increasingly see themselves as obedient pawns of the government and not as independent agents who will stand up for what they believe in regardless of the consequences.

Our federal government has acknowledged that politicians should not try to pick winners and losers in the economic marketplace, but persists in trying to do so in the marketplace of ideas. In the 2007 and 2008 budgets, the federal government dictated where new money for granting councils could be spent - ruling out the vast majority of researchers' work. In the 2009 budget, it restricted new social science humanities graduate scholarships to students "focused on business-related degrees."

That research funding has become politicized was also evident when the presidents of the three granting councils - the Natural Sciences and Engineering Research Council, the Social Sciences and Humanities Research Council and the Canadian Institutes of Health Research - failed to object when their budgets were cut, and when Genome Canada's president expressed concerns, then quickly retracted them. Canada's research funding agencies should be made arms' length from government.

[Hat Tip: T. Ryan Gregory: Genomicron]

Is Your Irony Meter Working?

Back in the days of newsgroups (last century) the howlers in talk.origins developed a running joke about irony meters. They were always being fried by outrageous comments from the anti-science creationists. New, more powerful, irony meters were needed every few months.

Here's a chance to calibrate your new irony meter.

The National Center for Science Education (NCSE) has just published a brief they submitted to the US Federal Government on the issue of scientific integrity [NCSE encourages federal scientific integrity].

Part of it reads ...

There is a long-running conflict over a creationist book being sold in the science section of bookstores at Grand Canyon National Park, creating a conflict between the scientifically-oriented presentations of Park Service staff and an implied Park Service endorsement of erroneous scientific views. The federal government should not lend its credibility to material which falsely claims scientific support for a 6000 year-old Earth or other attempts to masquerade religious apologetics as science. It is appropriate to discuss religious views in publications, presentations, and other educational settings, but the integrity of the scientific process is compromised when descriptions of religious views are not clearly distinguished from empirically tested scientific results.

Re-read that last sentence; "the integrity of the scientific process is compromised when descriptions of religious views are not clearly distinguished from empirically tested scientific results." I agree 100%; "The federal government should not lend its credibility to ... attempts to masquerade religious apologetics as science."

So how does that rule about integrity play out when leading scientific organizations like AAAS and NAS promote the compatibility of science and religion by endorsing and publicizing religious scientists in their official publications? Or how about the evolution display at the American Museum of Natural History?

What value registered on your irony meter?

[Image Credit: Wikipedia: Irony Meter]

Denyse O'Leary and Harun Yahya

Adnan Oktar is a Turkish creationist whose anti-evolution diatribes are usually published under the name Harun Yahya. Denyse O'Leary is a Canadian creationist who publishes anti-evolution diatribes under her own name.

I suppose it was only a matter of time before those two were attracted to one another. Denyse interviews Adnan Oktar on Uncommon Descent [Interview with Turkish Darwin doubter Adnan Oktar].

O’LEARY: How did you become interested in the evolution controversies? The conventional wisdom offered by many media sources in North America is that doubts about Darwin are a product of American evangelical Christianity in the deep rural South, and can only be understood with reference to that culture. Unless I have lost the plot, your doubts could not stem from that culture. From what, then, did they stem?

ADNAN OKTAR: I realized while I was still in high school that there was something odd about World War I, World War II and revolutions. Because people do not suddenly wake up one day and decide to start slaughtering their neighbors or ruining and devastating a country. I did some investigation and saw that the Darwinist materialist mindset lies behind all wars, revolutions and anarchy. I was terribly distressed by the way people were suffering so much, by the oppression and injustice they were being subjected to, and decided to wage an intellectual campaign against Darwinism to the utmost of my powers.

Amazing. It's really hard to decide which one is more wrong, although I must say I'm tilting toward Adnan Oktar. The idea that all wars were due to Darwinism—especially those fought during the expansion of the Ottoman Empire— is mind-boggling.

[Image Credit: Guide Martine]

Canadian Invasion

The Canadian invasion is proceeding as planned.

Most of the rest stops along the New York State Thruway have a Timmy's and you can find lots of them in the bigger cities. It won't be long before Starbucks is in trouble.

Note to my American friends ... be afraid ... be very afraid. Civilization is coming to America. You will be assimilated.

Wednesday, May 13, 2009

New York: Central Park

Nobel Laureate: Richard Ernst

The Nobel Prize in Chemistry 1991.

"for his contributions to the development of the methodology of high resolution nuclear magnetic resonance (NMR) spectroscopy"

Richard R. Ernst (1933 - ) won the Nobel Prize in Chemistry for important contributions to the technology of nuclear magnetic resonance (NMR) as a tool to understanding the three-dimensional structure of molecules.

The press release describes his work in some detail.
THEME:
Nobel Laureates

Revolutionary developments make a spectroscopic technique indispensable for chemistry

The 1991 Nobel Prize in Chemistry has been awarded to Professor Richard R. Ernst of the ETH, Zurich, for important methodological developments within nuclear magnetic resonance (NMR) spectroscopy. NMR spectroscopy has during the last twenty years developed into perhaps the most important instrumental measuring technique within chemistry. This has occurred because of a dramatic increase in both the sensitivity and the resolution of the instruments, two areas in which Ernst has contributed more than anybody else.

NMR spectroscopy is today used within practically all branches of chemistry, at universities as well as industrial laboratories. The method has its most important applications as a tool for the determination of molecular structure in solution. It can today be applied to a wide variety of chemical systems, from small molecules (e.g. drugs) to proteins and nucleic acids. Further, chemists use NMR to study interactions between different molecules (e.g. enzyme - substrate, soap - water), to investigate molecular motion, to get information on the rate of chemical reactions and for many other problems. The NMR technique is today also important in related sciences, such as physics, biology and medicine.

Background

The first successful NMR experiments were reported in 1945, by two independent groups in the USA (Bloch and co-workers at Stanford and Purcell with his group at Harvard). Their discovery was awarded a Nobel Prize in Physics in 1952. The NMR phenomenon can be explained in the following way. When matter is placed in a magnetic field, some of the atomic nuclei (e.g. nuclei of hydrogen atoms, called protons) behave like microscopic compass needles. These tiny compass needles (called nuclear spins) can, according to the laws of quantum mechanics, orient themselves with respect to the magnetic field in only a few ways. These orientations are characterized by different energy levels. The nuclear spins can be forced to jump between levels if the sample is exposed to radio waves of exactly specified frequency. The frequency is varied during the course of the experiment and, when it exactly matches the characteristic frequency of the nuclei (the resonance frequency), an electric signal is induced in the detector. The strength of the signal is plotted as a function of frequency in a diagram called the NMR spectrum. Around 1950, it was discovered that nuclear resonance frequencies depended not only on the nature of the atomic nuclei, but also on their chemical environment. The possibility of using NMR as a tool for chemical analysis soon became obvious and was mentioned by, among others, Professor Purcell in his 1952 Nobel lecture. A fundamental difficulty in the early days was the relatively low sensitivity of the NMR method.

A major breakthrough occurred in 1966 when Ernst (together with Weston A. Anderson, USA) discovered that the sensitivity of NMR spectra could be increased dramatically if the slow radiofrequency sweep that the sample was exposed to was replaced by short and intense radiofrequency pulses. The signal was then measured as a function of time after the pulse. The next pulse and signal acquisition were started after a few seconds, and the signals after each pulse were summed in a computer. The NMR signal measured as a function of time is not amenable to a simple interpretation (see Figure la). It is however possible to analyze what resonance frequencies are present in such a signal - and to convert it to an NMR spectrum - by a mathematical operation (Fourier transformation, FT) performed rapidly in the computer. The result of the Fourier transformation of Figure la is shown in Figure lb.

This discovery is the basis of modern NMR spectroscopy. The ten-fold, and sometimes hundred-fold, increase in sensitivity has made it possible to study small amounts of material as well as chemically interesting isotopes of low natural occurrence, e.g. carbon- 13. The enormous potential of the new technique - called FT NMR - quickly became obvious to NMR spectroscopists. The chemical research community got access to it in the early seventies through commercial FT NMR instruments. Nowadays, practically no other types of NMR spectrometer are manufactured.

By the end of the sixties, NMR spectroscopists had begun to use new magnet designs, based on superconducting materials, and the quality of spectra - expressed both in terms of sensitivity and resolution - improved quickly during the seventies. Consequently, more complex systems could be studied and more sophishcated questions answered. To move to very large molecules, macromolecules, another breakthrough was necessary, and this again carried the signature of Ernst. Inspired by a lecture of Jean Jeener, Belgium, at a summer school at the beginning of the seventies, Ernst and co-workers showed in 1975-76 how "two-dimensional" (2D) NMR experiments could be performed and demonstrated that 2D FT NMR opened entirely new possibilities for chemical research.

This 2D methods functions in the following way. Nuclear spins in a magnetic field are now subjected to sequences of radio-frequency pulses rather than to single pulses. The time course of the experiment is divided into four intervals. During the "preparation period", the equilibrium of the nuclear spin system is distorted by one or several pulses. This non-equilibrium is allowed to evolve for a certain time (the "evolution period"), after which the next series of pulses (the "mixing period") leads to the "detection period". Here the NMR signal is detected as a function of time in the same way as in ordinary, one-dimensional FT NMR. After this, one moves to the next preparation period and repeats the experiment with different evolution period. The change in the evolution period causes the signal measured during the detection period to change. One might say that the history of spins during the evolution period becomes encoded in the variation of the signal measured during the detection period. This gives a two-dimensional table with signal intensity as a function of both the point in time during the detection period and the length of the evolution period. Finally, the Fourier transformation is performed twice - with respect to both these time parameters - to obtain a two-dimensional frequency spectrum in the form of a map of the dependence of the signal intensity on two frequency parameters (denoted f1 and f2 in Figure 2).

Introduction of the second frequency dimension allows the spectral information to attain much higher resolution - like looking at the skyline of a mountain range and then looking at the whole range from an aircraft above. Depending on the design of the preparation and the mixing periods, one obtains a variety of 2D NMR experiments. Some are used to spread the information over two dimensions rather than one (separation of interactions) while others are designed to find which nuclei have some form of contact with each other (correlation of signals).

In the mid-seventies, Ernst also proposed a method of obtaining NMR-tomographic images which became one of the most common (the NMR tomography method as such was earlier realized by Lauterbur in the USA, Mansfield in England and others).

Since the mid-seventies, Ernst and co-workers have continuously and decisively contributed to the development of NMR spectroscopy, and in particular its two-, and more recently three- and multi-dimensional varieties. Applications of his methods were soon to come. For example, it has become possible over the past ten years to use NMR to determine the three-dimensional structure of organic and inorganic compounds as well as proteins and other biological macromolecules in solution with an accuracy comparable to what can be attained in crystals using X-ray diffraction. Interactions between biological molecules and other substances (metal ions, water, drugs) have also been studied in detail. Other important chemical applications are identification of chemical species (where NMR spectra act as the fingerprint of a molecule), studies of rates of certain chemical reactions and of molecular motions in the liquid state. In the border area between chemistry and biology, NMR is being used to study how metabolic processes are influenced by drugs, ischaemia etc. Ernst's own work often falls in the border area between chemistry and physics and can, if one so wishes, be treated as extremely elegant experimental verification of the correctness of quantum mechanics.

[Photo Credit: Science Festival]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Nobel Laureate: Harald zur Hausen

The Nobel Prize in Physiology or Medicine 2008

"for his discovery of human papilloma viruses causing cervical cancer"

Harald zur Hausen (1936 - ) won the Noble Prize in 2008 for discovering that a virus, human papilloma virus, causes cervical cancer. He also won a Gairdner Award in 2008.

Zur Hausen's discovery led eventually to the development of an HPV vaccine. Gardasil is the best known of the two vaccines on the market. Most doctors recommend that young girls be vaccinated.

Here's the 2008 press release on Zur Hausen.
THEME:
Nobel Laureates

Discovery of human papilloma virus causing cervical cancer

Against the prevailing view during the 1970s, Harald zur Hausen postulated a role for human papilloma virus (HPV) in cervical cancer. He assumed that the tumour cells, if they contained an oncogenic virus, should harbour viral DNA integrated into their genomes. The HPV genes promoting cell proliferation should therefore be detectable by specifically searching tumour cells for such viral DNA. Harald zur Hausen pursued this idea for over 10 years by searching for different HPV types, a search made difficult by the fact that only parts of the viral DNA were integrated into the host genome. He found novel HPV-DNA in cervix cancer biopsies, and thus discovered the new, tumourigenic HPV16 type in 1983. In 1984, he cloned HPV16 and 18 from patients with cervical cancer. The HPV types 16 and 18 were consistently found in about 70% of cervical cancer biopsies throughout the world.

Importance of the HPV discovery

The global public health burden attributable to human papilloma viruses is considerable. More than 5% of all cancers worldwide are caused by persistent infection with this virus. Infection by the human papilloma virus is the most common sexually transmitted agent, afflicting 50-80% of the population. Of the more than 100 HPV types known, about 40 infect the genital tract, and 15 of these put women at high risk for cervical cancer. In addition, HPV is found in some vulval, penile, oral and other cancers. Human papilloma virus can be detected in 99.7% of women with histologically confirmed cervical cancer, affecting some 500,000 women per year.

Harald zur Hausen demonstrated novel properties of HPV that have led to an understanding of mechanisms for papilloma virus-induced carcinogenesis and the predisposing factors for viral persistence and cellular transformation. He made HPV16 and 18 available to the scientific community. Vaccines were ultimately developed that provide ≥95 % protection from infection by the high risk HPV16 and 18 types. The vaccines may also reduce the need for surgery and the global burden of cervical cancer.

[Photo Credit: IBMLive]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

New York City

New York: American Museum of Natural History

Guess who I saw in the American Museum of Natural History in New York?

No, I'm not thinking of a family of stuffed elephants or a giant blue whale. I'm not even thinking of the butterflies in the butterfly conservatory. The people who I'm thinking about are much more exciting.

My friend and I visited the evolution display. It was really excellent. The dioramas and descriptions described a no-holds-barred version of evolution complete with supporting evidence from fossils, DNA sequences, and biogeography. The statements were factual (mostly) and scientific. No dumbing down and no pulling punches.

I remarked to my friend that this was unusual and I would be surprised if there weren't some "disclaimers" at the end of the display.

Sure enough, just before reaching the end we saw some familiar faces. There were Ken Miller, Francis Collins, and Genie Scott in full length videos explaining why evoluton and religion are compatible. I waited to see if PZ Myers or Richard Dawkins would put in an appearance—no such luck.

We didn't even see Neil deGrasee Tyson in the video in spite of the fact he's the director of the Hayden Planetarium at the museum. Niles Eldredge famous evolutionary biologists and curator of paleontology at the museum wasn't there either. I wonder why?

Add the American Museum of Natural History to the list of accommodationists. There was no compelling reason to interrupt an otherwise excellent scientific display with a sop to religion.

Britich Columbia Rejects Electoral Reform

In yesterday's election the people of British Columbia were asked to choose between the old first-past-the post electoral system and a new single transferable vote system. The referendum question was ...

Which electoral system should British Columbia use to elect members to the provincial Legislative Assembly? The existing electoral system (First-Past-the-Post) or the single transferable vote electoral system (BC-STV) proposed by the Citizen's Assembly on Electoral Reform.

Up until the beginning of May, it was widely anticipated that more than 60% would vote for STV, thus ensuring that a fair electoral system would become law in British Columbia.

The actual result was a disaster for electoral reform. Only 39% of the voters favored STV while 61% voted to retain the old unfair first-past-the-post system [Elections BC].

This is a major defeat. It will make it much more difficult to get electoral reform passed in Ontario or any other province. As usual, North Americans are much more conservative than the civilized world.

Is Acupuncture Better than Toothpicks?

Orac is at it again. He describes a pretty good study of the possible effects of acupuncture on lower back pain [Another acupuncture study misinterpreted]. The study showed that patients who got a sham procedure using toothpicks instead of needles reported the same "cure" as those who got two different versions of acupuncture.

In other words, acupuncture doesn't work. The scientific evidence is conclusive. Acupuncture is associated with a potent placebo effect but that's all. Patients can't tell the difference between needles and toothpicks. As long as they think they're getting the full-blown acupuncture treatment they'll report an improvement in lower back pain.

Here's the description of the toothpick technique that "cures" back pain.

Simulated acupuncture. We developed a simulated acupuncture technique using a toothpick in a needle guide tube, which was found to be a credible acupuncture treatment by acupuncture-naïve patients with back pain.Simulating insertion involved holding the skin taut around each acupuncture point and placing a standard acupuncture needle guide tube containing a toothpick against the skin. The acupuncturist tapped the toothpick gently, twisting it slightly to simulate an acupuncture needle grabbing the skin, and then quickly withdrew the toothpick and guide tube while keeping his or her fingers against the skin for a few additional seconds to imitate the process of inserting the needle to the proper depth. All acupuncture points were stimulated with toothpicks at 10 minutes (ie, the acupuncturist touched each acupuncture point with the tip of a toothpick without the guide tube and rotated the toothpick clockwise and then counterclockwise less than 30°) and again at 20 minutes just before they were "removed." To simulate withdrawal of the needle, the acupuncturist tightly stretched the skin around each acupuncture point, pressed a cotton ball firmly on the stretched skin, then momentarily touched the skin with a toothpick (without the guide tube) and quickly pulled the toothpick away using the same hand movements as in regular needle withdrawal. The acupuncturists simulated insertion and removal of needles at the 8 acupuncture points used in the standardized treatment.

Just about anyone could be trained to do this. Think of how much unnecessary back pain could be eliminated if spouses and friends would just poke each other with toothpicks!

I think I'll ask Ms. Sandwalk to try it next time my back hurts.

Monday's Molecule #121: Winner

UPDATE:The image is a 2D Nuclear magnetic resonance spectrum of cane sugar from the Nobel website. This kid of image can only be produced by mathematically transforming the primary data to create a multidimensional representation. Richard Ernst discovered the Fourier transform method that led to solving three dimensional structures by NMR. He won a Nobel Prize in 1991.

This week's winner is Michael Clarkson of Waltham MA (USA). The dominance of Canadians is coming to an end.

This is a true representation of the structure of a biological molecule but I don't expect you you to guess the molecule. Instead, you have to explain what this image is depicting and how it relates to a Nobel Laureate.

There is one Nobel Laureate who is most closely identified with this particular type of image. You have to identify the Nobel Laureate and what the prize was for. Be careful, because I'm looking for the pioneer in this field and not for other Nobel Prize winners who may have come later. Be sure to check the list of previous Nobel Laureates on Sandwalk.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison and Adam Santoro of the University of Toronto.

The Canadians are still ahead in the competition between Canadians the rest of the world but Dima and Laura are at least keeping it from being a total rout.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

~~Comments will be blocked for 24 hours.~~ Comments are now open.

Tuesday, May 12, 2009

Monday's Molecule #121

This is a true representation of the structure of a biological molecule but I don't expect you you to guess the molecule. Instead, you have to explain what this image is depicting and how it relates to a Nobel Laureate.

There is one Nobel Laureate who is most closely identified with this particular type of image. You have to identify the Nobel Laureate and what the prize was for. Be careful, because I'm looking for the pioneer in this field and not for other Nobel Prize winners who may have come later. Be sure to check the list of previous Nobel Laureates on Sandwalk.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison and Adam Santoro of the University of Toronto.

The Canadians are still ahead in the competition between Canadians the rest of the world but Dima and Laura are at least keeping it from being a total rout.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

E.O. Wilson in New York

It was Saturday morning and I was in the offices of the New York Academy of Sciences on the 40th floor of 7 World Trade Center. The view to the East was spectacular. We could see the Brooklyn bridge and the 59th Street bridge with Brooklyn and Queen's in the background.

I love cities, I love the tall buildings and the hustle and bustle of the street life.

E.O. Wilson was about to kick off the opening session of The Two Cultures in the 21st Century. I had never heard him in person so I grabbed a good seat and settled down.

Most of his talk was about imaging the brain, behaviorial psychology, and evolutionary psychology. His main point was that scientists are learning a lot about how the brain works and this brings together the humanities and science. E.O. Wilson favors consilience.

Let me give you one example from his talk to illustrate the concept. Wilson talked about a study that was done to determine the ideal environment for humans. People were asked to identify their favorite scenes and the results were used to derive a composite view of what the ideal human environment would look like.

Wilson illustrated it with a slide taken from the third or fourth floor of the John Deere headquarters in Illinois. The view showed extensive grasslands with some water in the foreground. The trees had large branches that were almost parallel to the ground. Massive abstract sculptures evoked an image of large animals.

According to Wilson, this idealized environment is an ancient memory of the environment where we evolved. Our ancestors lived in caves on a cliff side overlooking a savanna full of large animals. The trees of the savanna have branches that are almost parallel to the ground. We like to have water nearby. This is why the typical modern human prefers that type of environment. Science and beauty come together.

Here's how Wilson describes it in The Creation: An Appeal to Save Life on Earth pp. 66-67

…Researchers have found that when people of different cultures, including those of North America, Europe, Asia and Africa, are given freedom to select the setting of their homes and work places, they prefer an environment that combines three features. They wish to live on a height looking down and out, to scan a parkland with scattered trees and copses spread before them, closer in appearance to a savanna than either a grassland or a closed forest, and to be near a body of water, such as a lake, river, or sea. Even if all these elements are purely aesthetic and not functional, as in vacation homes, people who have the means will pay a very high price to obtain them.

There is more. Subjects in choice tests prefer their habitation to be a retreat, with a wall, cliff, or something else solid to the rear. They want a view of fruitful terrain in front of the retreat. They like large animals scattered thereabout, either wild or domestic. Finally, they favour trees with low horizontal branches and divided leaves. It is probably not a coincidence that some people, I among them, consider the Japanese Maple the world’s most beautiful tree.

These quirks of human nature do not prove but are at least consistent with the savanna hypothesis of human evolution. Supported by considerable evidence from fossil record, this interpretation holds that human beings today still choose the habitats resembling those in which our species evolved in Africa during millions of years of prehistory.

I realized then and there that I was a strange sort of human. My love of cities must be some kind of aberration. I also realized in an instant that all of my mother's ancestors from the past 2000 years must have been desperately unhappy. They all come from Northern Europe where they lived in clusters of small farms in rolling hills covered in dense forest. The only thing they had going for them was the presence of large animals in the barns. How sad.

[Photo Credit: ©John Deere (John Deere Attractions)]

New York City: Theater and Dinner

The Human Genome Sequence Is not Complete

The latest version of the human genome sequence is called Build 36 or GRCh37. Here's an overview from the Genome Reference Consortium.

The large red triangles represent regions where there is a lot of variability so that no single representation of the genome sequence will describe a majority of humans.

The black regions represent parts of the chromosomes that have not been sequenced and assembled into long stretches (contigs) of reliable sequence. Most of the unsequenced regions are at centromeres, or telomeres, or on the Y chromosome. These regions consist of thousands of copies of highly repetitive DNA. It is impossible to assemble these repetitive sequences.

Scientists are urging that more attention be focused on completing the chimpanzee and macaque genome sequences. We have been waiting a long time for the draft sequences of those genomes to be finished. The explosion of data on the human genome can only be realistically evaluated by comparing it to our closest relatives. (For example, are human non-coding RNAs conserved in primates?)

The fact that the human genome is not complete is not a problem. We know what's in the repetitive sequence regions even though we don't know exactly how it is arranged. The effort required to finish of the last bit is probably not as important as getting a final draft of other sequences.

Sandra Porter wonders Why don't we finish the human genome first?.

Jason Rosenhouse Doesn't Understand Pluralists

Jason Rosenhouse has posted some comments on a recent book review by Richard Lewontin. In that book review, Lewontin—who along with Gould is the co-author of the spandrels paper—questions the emphasis on natural selection and the use pf "Darwinism" as a synonym for evolution. Read Lewontin on Darwin to see what Jason thinks of the book review.

I want to focus on a specific question that Jason Rosenhouse asks.

I've never really understood what it is exactly that anti-selectionists are complaining about. If they agree that complex adapations arise as the result of gradual accretion mediated by natural selection, then I fail to see how they are really so different from people like Richard Dawkins or Daniel Dennett (two people often described as being beknighted uber-selectionists). If they do not agree then I would like to hear their proposed alternative mechanism.

The original paper by Gould and Lewontin, The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme, explains the problem very well. The authors begin their criticism with ...

We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm. It is rooted in a notion popularized by A.R. Wallace and A. Weismann, (but not, as we shall see, by Darwin) toward the end of the nineteenth century: the near omnipotence of natural selection in forging organic design and fashioning the best among possible worlds. This programme regards natural selection as so powerful and the constraints upon it so few that direct production of adaptation through its operation becomes the primary cause of nearly all organic form, function, and behavior. Constraints upon the pervasive power of natural selection are recognized of course (phyletic inertia primarily among them, although immediate architectural constraints, as discussed in the last section, are rarely acknowledged). But they are usually dismissed as unimportant or else, and more frustratingly, simply acknowledged and then not taken to heart and invoked.

The anti-selectionists—I am one—do not question the fact that adaptations are produced by natural selection. What we question is whether everything in evolution is an adaptation. We question those who think that "evolution" and "natural selection" are synonyms. And since "Darwinism" is equivalent to evolution by natural selection we question whether evolution is the same as Darwinism.

We pluralists like to point out that much of evolution is due to random genetic drift. Since Darwin's name is not associated with the theory of evolution by random genetic drift, it is inappropriate to say that all of evolution is Darwinist.

It's not that complicated. It was all explained in the classic spandrels paper published 30 years ago. Complex biological structures may be due entirely to adaptation, or they may be mostly an accident that's arisen by random genetic drift, or they may be due to combinations of drift and selection.

Friday, May 08, 2009

What do protein crystallographers dream of?

"What do protein crystallographers dream of?" is the question asked by Ananyo Bhattacharya in an article published in Nature [Protein structures: Structures of desire].

The structures of many protein complexes have been determined but crystallographers have a list of holy grails that, so far, have eluded them. It's an interesting list and one that I mostly agree with. Can you identify the structure shown here in cartoon form?

One glaring omission is pyruvate dehydrogenase. Lot's of people want to see that structure. Other notable omissions include complex I of the membrane-associated electron transport chain and the protein import complex of the endoplasmic reticulum. Don't protein crystallographers dream of those?

The Biology Textbooks Are Wrong?

The other day I suggested that Casey Luskin was probably just ignorant. Unlike other creationists, he problably isn't a liar. Today I'm not so sure.

What is it with FOX news?

Thursday, May 07, 2009

Win Free Prizes from Denyse O'Leary

Every week there are dozens of people who try to guess Monday's Molecule and win a free lunch with me. Now, that's a valuable prize—it's no wonder that so many people are trying to win.

Now you've got another chance to win valuable prizes. Denyse O'Leary is giving out prizes for people who comment on Uncommon Descent [Earn free stuff!: The Uncommon Descent Contest].

What are the prizes?

10 DVDs of Expelled,courtesy the producers.
10 DVDs of Privileged Planet, courtesy the producers.
5 subscriptions, including back issues, to the excellent Christian/theistic science and culture mag, Salvo, complete with recent back issues, courtesy the editor-in-chief.

Looks like I've got serious competition!

Here's the first contest question: Does the multiverse help science make sense - or simply destroy science?. Hmmm ... I wonder what the right answer is?

Casey Luskin Writes About the Universal Common Ancestor

Casey Luskin is writing about the tree of life and the universal common ancestor. The second installment in a series of five posting is here.

When speaking to the public, evolutionists are infamous for overstating the evidence for universal common ancestry. For example, when speaking before the Texas State Board of Education in January, 2009, University of Texas evolutionist biologist David Hillis cited himself as one of the “world’s leading experts on the tree of life” and later told the Board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. But this is not accurate. Indeed, in the technical scientific literature, one finds a vast swath of scientific papers that have found contradictions, inconsistencies, and flat out failures of the molecular data to provide a clear picture of phylogenetic history and common descent.

Indeed, the cover story of the journal New Scientist, published on the very day that Dr. Hillis testified, was titled, “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’ gross oversimplification of molecular systematics, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:

It's true that things are very confusing at the base of the tree of life. The evidence indicates that genes were frequently exchanged between primitive prokaryotic species and this means there is no single tree that represents all of life.

But this doesn't negate the idea of a universal common ancestor. The origin of life could still be a unique event that gave rise over millions of years to many different descendants that subsequently exchanged genes. Or, there may have been a few independent origins of life.

The available evidence shows that most fundamental properties of life are shared by all living things (e.g. basic metabolic pathways, genetic code). This is consistent with a unique origin of life but it's also consistent with multiple origins as long as only one version of each process has survived. The odds favor a single origin and a universal common ancestor.

What's interesting about Luskin's article is that he is hopelessly confused about the difference between a phylogenetic tree and the origin or life. He seems to think that a bushy tree with many interconnecting branches rules out a universal common ancestor. I don't know what he postulates in its place unless the idea of God creating three or four different primitive prokaryotes is what appeals to him more than God just doing it once.

Intelligent Design Creationists come in many different flavors. Often it's hard to decide whether they are being deceptive (lying) or just ignorant. I think that Casey Luskin is just ignorant. He finds it difficult to make a coherent argument and he doesn't take the time to learn more about his subject. In that sense, he's much less dangerous than Jonathan Wells.

Call a Canadian!!

Dear Americans,

Have you ever thought about asking an average Canadian what they think of their health care system? Read Call a Canadian on Effect Measure.

Oops! Did New Scientist Goof Again?

New Scientist published an article on Science and art: Still two cultures divided?.

The journal invited six people to comment on the two cultures. Here's the list ....

Stefan Collini is a professor of literature and intellectual history at the University of Cambridge. He edited The Two Cultures (1993, CUP)
Susan Haack is a professor of philosophy and a professor of law at the University of Miami, Florida
Harry Collins is professor of sociology at Cardiff University in the UK
Mary Midgley is a philosopher and writer
Sandra Harding is a philosopher and professor of education at the University of California, Los Angeles
A. C. Grayling is a professor of philosophy at Birkbeck, University of London

A perceptive commenter (Khoo) asks, "Why was an entire article written about the divide between the arts and the sciences, and not a single physical scientist or mathematician interviewed? Does the author believe these scientists have nothing to say about the arts?"

Good point. A classic demonstration of the two cultures in action.

Wednesday, May 06, 2009

Atheists Serve the Devil!

Who knew? I wonder what the Devil eats for lunch? If I'm going to serve him I'd better find out.

Is he a big tipper?

This is Pat Robertson responding to a question. A caller wants to know how she, a Christian, can get along with her boyfriend, an atheist. Can you guess how the good Christian responds? Think about it, then watch.

[Hat Tip: Friendly Atheist]

How to Frame a Null Hypothesis

A reader has alerted me to an article by Michael White at Adaptive Complexity: Genomic Junk and Transcriptional Noise.

With hot, new technologies, biologists are taking higher-resolution snapshots of what's going on inside the cell, but the results are stirring up controversy. One of the most interesting recent discoveries is that transcription is everywhere: DNA is transcribed into RNA all over the genome, even DNA that has long been thought to have a non-functional role. What is all of this transcription for? Does the 'dark matter' of the genome have some cryptic, undiscovered function?

Unfortunately, in all of the excitement over possible new functions, many biologists have forgotten how to frame a null hypothesis - the default scenario that you expect to see if there is no function to this transcribed DNA. As a result, the literature is teeming with wild, implausible speculation about how our excess DNA might be beneficial to us.

So here, let's step back and look at what we expect from DNA when it's playing absolutely no functional role; in other words, let's look at the null hypothesis of genomic junk and transcriptional noise. We can then take our null hypothesis and use it to look at a fascinating new study of how genomic parasites sculpt transcription in our cells.

If you are interested in what's wrong with science these days then you must read his article.

The point is not whether you believe that all transcription is adaptive and functional, or whether you believe that most of it is noise. The real point is that it is very bad science to ignore the null hypothesis and publish naive speculation as if it were the only possible explanation.

Whenever you see a paper that fails to address the null hypothesis you can be sure that you are reading bad science. Everything else in the paper is suspect.

The key fact that most scientists are overlooking is that RNA polymerase and the various transcription factors must bind non-specifically at thousands of sites in a random sequence of junk DNA. This is just basic biochemistry of the sort that should be taught in undergraduate classes. Transcription will be initiated by accident at some of these sites even though they are not functional promoters. Again, this is basic biochemistry.

[Image Credit: Horton et al. Principles of Biochemistry 4/e p.657]

Two Cultures in New York City

Tomorrow is the 50th anniversary of a lecture by C.P. Snow on The Two Cultures.

He said,

A good many times I have been present at gatherings of people who, by the standards of the traditional culture, are thought highly educated and who have with considerable gusto been expressing their incredulity at the illiteracy of scientists. Once or twice I have been provoked and have asked the company how many of them could describe the Second Law of Thermodynamics, the law of entropy. The response was cold: it was also negative. Yet I was asking something which is about the scientific equivalent of: 'Have you read a work of Shakespeare's?'

I now believe that if I had asked an even simpler question — such as, What do you mean by mass, or acceleration, which is the scientific equivalent of saying, 'Can you read?' — not more than one in ten of the highly educated would have felt that I was speaking the same language. So the great edifice of modern physics goes up, and the majority of the cleverest people in the western world have about as much insight into it as their Neolithic ancestors would have had.

Not much has changed in fifty years. We still live in a society that is at best scientifically illiterate and, at worst, anti-science.

Tomorrow I'll be on my way to New York City to attend a conference on The Two Cultures in the 21st Century. The meeting was organized (in part) by Chris Mooney and Sheril Kirshenbaum. It begins with a keynote address by E.O. Wilson followed by four symposia on ...

The Two Cultures in Historical Perspective: From Aristotle to "Science Wars" and the "Third Culture"
How to More Effectively Communicate Science Issues to the Public
Restoring Science to Its Rightful Place in Politics
A Better Future through Science Citizenship

Carl, (I Got Your Two Cultures Right Here), Zimmer will be there.

We all have our stories and our examples of the problem. The one I like to tell is the story about a group of knowledgeable adults at a cocktail party when something mathematical comes up in the conversation. Chances are someone is going to brag about how much they feared math in schools and how little they know about the subject. This will undoubtedly get murmurs of sympathy from many people.

Now imagine that the group was discussing modern literature and I said something similar; "I hated literature in school, I never 'got' the point of these modern writers and why they are so famous. Literature was way too hard for me so I stopped taking literature courses as soon as I could." Do you think there would be murmurs of sympathy and understanding? I doubt it. The group would probably think I'm stupid.

The two cultures problem will only be solved when the proper response to someone who claims to be an idiot in mathematics is the same as to someone who claims to be an idiot about art and literature.

The other problem is when people claim to be knowledgeable about science when they aren't. Chris Matthews of MSNBC has the right idea when he attacks Rep. Mike Pence (Indiana-R) ["You Want to Educate Americans About Science; Do You Believe In Evolution?"]. We can't allow people to pretend they know about science when they reject the core principles of science. If you are ignorant about science then you are ignorant, period.

Today's issue of New Scientist has an article on Science and art: Still two cultures divided? .

On the Origin of Chloroplasts

We know that many species contain chloroplasts. In most cases, these species descend directly from a common ancestor that acquired the chloroplast through an endosymbiotic relationship with a cyanobacterium. The endosymbiotic origin of chloroplasts from cyanobacteria is not in doubt.

What is in doubt is whether the original endosymbiosis happened just once or whether there are multiple independent origins of chloroplasts. We also know that some species acquired chloroplasts by fusing with another chloroplast-containing eukaryotic species. How many examples of secondary acquisition are required to explain the phylogeny of species that contain chloroplasts? Are there tertiary and quaternary acquisitions?

Christopher Taylor of Catalogue of Organisms has posted a nice summary of the problems in this field at Crossing the Algal Divide. If you want to keep up with one of the important problems in evolution then this is an excellent place to start.

[Photo Credit: micro*scope]

Tuesday, May 05, 2009

Monday's Molecule #120: Winners

UPDATE: The image depicts the genome of a human papillomavirus. The Nobel Laureate is Harald zur Hausen.

This week's winners are Dima Klenchin of the University of Wisconsin and Adam Santoro of the University of Toronto. They were the first of many who got the right answer. This surprises me 'cause I thought it would be harder. I didn't realize how easy it was to get the molecule by searching for "E6" or "E7."

This is a cartoon showing the genes present in a particular DNA molecule. Your task is to identify the kind of DNA molecule being depicted.

There is one Nobel Laureate who is most closely identified with this particular type of molecule. You have to identify the Nobel Laureate and what the prize was for.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, and Stefan Tarnawsky of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

~~Comments will be blocked for 24 hours.~~ Comments are now open.

How to Teach Evolution?

You're not going to believe this. The National Institute of General Medical Sciences (NIGMS), the Office of Science Education (OSE), and the National Academy of Sciences (NAS) sponsored Matt Nisbet to give a lecture on Communicating About Evolution.

Who knew that Matt was an expert on evolution? Here's what Matt says about the lecture on his website [Video for NAS Lecture: Communicating about Evolution].

For readers of this blog and followers of the "Framing Science" thesis, the National Academies presentation is the most detailed lecture I have given on how to effectively engage with the public on the relationship between science and religion and the specific topic of evolution. The lecture follows closely articles and book chapters that I have previously published or that are forthcoming.

Near the end of his lecture Matt defends the "frame" of emphasizing that religion and science are not in conflict (~50 minutes). In this context, frame is not much different than spin and spin is not much different than lie. The truth is that science and religion are often in conflict. Any statement to the contrary is not the truth.

Matt's views about framing have been so thoroughly rejected by scientists that The National Institute of General Medical Sciences (NIGMS), the Office of Science Education (OSE), and the National Academy of Sciences (NAS) should be ashamed of themselves.

See Matt Nisbet Endorses Francis Collins for Presidential Science Advisor - The Kiss of Death for an example of how Nisbet wants to frame the debate.

Do High School Student Want to Become Scientists?

Do High School Student Want to Become Scientists? the answer is, no [Is Canada losing the lab-rat race?].

"Look up 'scientist' on Google," the 16-year-old says, "and you will see someone in a lab coat." At the moment, she is considering something with more immediate results, such as physiotherapy.

Ask her biology classmates at Colonel By Secondary School in Ottawa if any of them want to be scientists and only a few tentative hands flicker up. What's worrying is that this is no average high-school science class. It is part of the International Baccalaureate program, chosen from a large pool of applicants. These are students who spend half of their time in labs, working through experiments, not dozing off during lectures - the kind of education most scientists wish they had had. If any group should be producing lab-coat keeners, it should be this one.

Julia Dutaud, 16, sitting in the back in her school-rugby T-shirt, would like to study environmental science - a field growing as rapidly as any - but she wonders if she could make a good living at it: "Going into science would be a nice thing to do," she says. "But we aren't sure how much opportunity we would get after university."

Half the students are planning to be doctors instead, a profession they and their parents consider more stable.

I don't think this is a new problem. Back in the olden days, there also weren't a huge number of high school students who wanted to be scientists. Why should there be a significant number in a typical high school class? At my university there are about 8,000 students entering first year and about 400 or so want to pursue a career in science. That's about right—half of them (200) will be able to enter graduate school when they graduate and that's also about right. It means that a typical high school science class of 25 students will likely have only two or three who want to be scientists.

It would be a disaster if half of every high school science class wanted to become scientists because the vast majority would be disappointed.

There's another problem not covered in the Globe and Mail article. In my experience, many students don't begin to understand what a scientist is until they get to university and start seeing them in their natural environment. A surprising number of high school students think you have to be a physician in order to do the cool research on genes and diseases. It's only after they get to university that they learn the difference between a physician and a scientist.

When did you, dear reader, first develop a serious interest in science? Was it in high school or university? Is it a problem that there aren't more high school students who want to become scientists?

Science Education in Alberta

The Alberta legislature is considering a law that allows parents to pull their children out of certain classes if those classes conflict with the family's religion. Many people interpreted this to mean that parents could take their children out of biology classes when evolution is being taught [see Don't Like Evolution in Alberta?].

According to an article in The Globe and Mail this may have been an over-reaction [Alberta law imperils teaching of 'religious' topics like evolution, critics fear]. While the opposition parties are incensed and the school teachers are angry, it appears that there is at least one senior government official who knows the difference between science and religion.

Frank Bruseker, head of the Alberta Teachers' Association, said he is also concerned about what the new rules could mean.

He is worried that some parents might think mentioning different classes of worms would constitute a reference to evolution.

And he said no discussion of ancient geologic formations can be had without mentioning the world is billions of years old, much more than a literal reading of the Bible would suggest.

Meanwhile, history and literature from around the world are full of references to religious upheaval.

"Religion is kind of a fuzzy thing, in a sense, in that what some people see as religion others might not," Mr. Bruseker said.

Opposition parties have hammered the government on the issue, saying the province is headed back to the time of the 1925 Scopes trial, in which a high school biology teacher in Tennessee was tried for teaching Darwin's theory of evolution.

Premier Ed Stelmach conceded to reporters last week that the provision could be used to pull students out of classes dealing with evolution if parents preferred their kids be taught what's in the Bible instead.

"The parents would have the opportunity to make that choice," he told a news conference.

But Lindsay Blackett, the minister responsible for human rights, said in an interview that the intention of the law is to allow parents to pull children out only when the curriculum specifically covers religion, something that happens for a few hours each school year.

"It's talking about religion [such as] Hindu, or Muslim, or that type of religion, not ... the curriculum with respect to, for instance, evolution," he said.

"That's science and we're not arguing science."

I hope he (Blackett) is right and not the premier. I hope the new legislation will contain an amendment making it clear that students cannot be taken out of science classes when evolution is covered. It's nice to see so many teachers and politicians in Alberta standing up for science.

[Photo Credit: Minister of Culture and Community Spirit]

Politics and the Judicial Branch in America

Since America is a "nation of laws" it becomes very important to pass the "right" laws and to make sure that the American Supreme Court upholds them. To this end, each side of an issue wants to stack the Supreme Court with their sympathizers. Now that one of the members of the Supreme Court has retired, the lobbying to replace him has begun.

Eddie Tabash is very interested in the separation of church and state issue and he wants the next Supreme Court justice to be sympathetic to his point of view on the law. Apparently, there are well-qualified judges who would not be sympathetic, so the nomination process becomes highly politicized. Apparently, the Democrats want a judge who will agree with Tabash while the Republicans want a judge who might favor different laws.

Tabash has written a special article on RichardDawkins.net explaining how the process works [ It happened. There is now a Supreme Court vacancy]. It's very helpful for those of us in other countries. The politicization of the Judicial Branch of government seems very bizarre.

[Photo Credit: Tim Dillon, USA TODAY]

Monday, May 04, 2009

Monday's Molecule #120

This is a cartoon showing the genes present in a particular DNA molecule. Your task is to identify the kind of DNA molecule being depicted.

There is one Nobel Laureate who is most closely identified with this particular type of molecule. You have to identify the Nobel Laureate and what the prize was for.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, and Stefan Tarnawsky of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

Sunday, May 03, 2009

Theistic Evolution: How Does God Do It?

Theistic Evolution is a form of creationism that limits God's involvement in the creation event. The chief limitation is that most of God's activity have to be consistent with the facts of evolution.

Francis Collins has created a website devoted to his concept of BioLogos, which, it turn out, is just another word for Theistic Evolution. The website is funded by a grant from the John Templeton Foundation.

Many of us have difficulty understanding how a personal God can be involved in guiding evolution without violating the laws of physics and chemistry. In other words, how is Theistic Evolution/BioLogos compatible with science? This is a key question since we know that major scientific organizations (AAAS, NAS, NCSE) support the notion that science and religion are compatible. In fact, they explicitly support Francis Collins and Theistic Evolution.

Let's see how science and religion are compatible by looking at Question 14 on the BioLogos website [What role could God have in evolution?].

Divine Action is defined as God’s interaction with creation. Due to the understanding that evolution accounts for the diversity of present life forms, it might appear God played no role in the process of evolution. (See Question 26 about The Complexity of Life.) Clearly this contradicts the central doctrine of creation for many faiths. Christianity, for example, professes a God actively involved in creation. Many faiths share the concept of an interactive God, or theism. The opposing belief — the belief in an uninvolved, disinterested God — is deism.

Collins sees this a a major problem. According to him, Christians believe in creation and a strictly scientific explanation of evolution seems incompatible with this belief.

Elsewhere on the website, Collins makes it clear that theism is not deism and his view of Theistic Evolution/BioLogos is not deistic. So how does he solve the problem?

Any God worthy of the name has to be capable of miracles, and each of the great Western religions attributes a number of very special miracles to their conception of God. What can science say about a miracle? Nothing. By definition, the miraculous is beyond explanation, beyond our understanding, beyond science.

Ken Miller in "Finding Darwin's God" p. 239Well, it's not very clear to me. There is some hand-waving and some backhanded suggestions but nothing specific is described. In this sense, the Francis Collins version of Theistic Evolution is similar to that of Ken Miller in Finding Darwin's God. Here's the BioLogos version..

Even before Darwin’s contribution to biology, the scientific revolution in physics marked a tremendous advance in our understanding of the world. Scientists discovered that the world’s behavior could be explained and predicted with great accuracy on the basis of physical laws. Nature, as understood at the time, appeared to reliably follow a set of fundamental rules. For example, the motion of planets could be explained as a necessary result of their obedience to the force of gravity. This understanding of the world lent itself to the belief in a rational, consistent creator.

But, as Polkinghorne puts it, these laws might also come across as “a gift from the Greeks.”5 Given a second look, they challenge basic theism. For as much as these laws signify a rational creator, their trustworthiness could also imply God’s absence. After all, if the laws of nature can explain almost any phenomenon, how is God involved? In order to understand how God could take an active role, or how the world could have any inherent freedom, the laws of nature must be somehow open or flexible. The world’s future cannot be entirely determined or predictable from any given moment.

This is the potential area of conflict. If science says that evolution obeys the laws of physics and chemistry then there's no room for an interventionist God without violating those rules. And if your God does that then there's a conflict between science and religion. They are not compatible.

What to do? Miller and Collins, and many other theists, opt for a solution where God can intervene at the quantum level without ever being detected. Thus, nature only appears to obey the fundamental laws of physics and chemistry because God is clever enough to disguise his interventions.

The mechanical worldview of the scientific revolution is now a relic. Modern physics has replaced it with a very different picture of the world. With quantum mechanical uncertainty and the chaotic unpredictability of complex systems, the world is now understood to have a certain freedom in its future development. Of course, the question remains whether this openness is a result of nature’s true intrinsic chanciness or the inevitable limit to humans’ understanding. Either way, one thing is clear: a complete and detailed explanation or prediction for nature’s behavior cannot be provided. This was already a problem for Newtonian mechanics; however, it was assumed that in principle, science might eventually provide a complete explanation of any natural event. Now, though, we see that the laws of nature are such that scientific prediction and explanation are ultimately limited.

It is thus perfectly possible that God might influence the creation in subtle ways that are unrecognizable to scientific observation. In this way, modern science opens the door to divine action without the need for law breaking miracles. Given the impossibility of absolute prediction or explanation, the laws of nature no longer preclude God’s action in the world. Our perception of the world opens once again to the possibility of divine interaction.

Despite the uncertainty and unpredictability of the world, we are not forced to reject the earlier understanding of God’s creation as consistent and reliable. After all, the world still exhibits the same orderly behavior that inspired so many faithful scientists of earlier centuries. Regardless of the irregularity of tiny,quantum mechanical, or complex, chaos theoretical, systems, the sun stills rises and sets, the tides ebb and flow, and objects fall to the ground. Nature is reliable enough to reflect God’s faithfulness yet flexible enough to permit God’s involvement.

So this is how to make science and religion compatible. Let's restate it so that everyone can grasp the argument,

"... modern science opens the door to divine action without the need for law breaking miracles. Given the impossibility of absolute prediction or explanation, the laws of nature no longer preclude God’s action in the world.."

On the surface it seems to work since, by definition, all of God's interventions and guidance are undetectable. Therefore, there can't be any obvious conflict between the purely modern scientific view of evolution and creationism.

Personally, I don't think you can have your cake and eat it too. Once you start attributing events to God's intervention you are conflicting with a strictly materialistic interpretation of those same events. It doesn't matter whether your God is extremely careful to fool scientists into thinking that evolution is natural. The very act of postulating divine intervention in the natural world is not compatible with the scientific way of knowing.

Here's the bottom line, according to Francis Collins.

Our modern understanding of physical laws combined with a proper understanding of God’s relationship to time can be synthesized into a robust theistic worldview. Darrel Falk provides the following perspective:
“The Bible tells us that God created, but it does not tell us how, and we need to be careful that we do not force the God of the Universe into one of our human molds. […] What do we learn about the nature of God’s activity from studying the Bible? One thing we learn is that God builds freedom into His creation. […] Just as God builds freedom into our lives today, so freedom may well be a central component of God’s biological world as well. This is not to say that God is not playing a supervisory role in creation in a manner resembling the role God plays in my life and yours. But there is no a priori scriptural reason to assume that the biological world was created one species at a time by the God of the Universe “pushing creation buttons” each time he wanted a new species. […] God’s spirit guides the progression of life. His presence is never far from creation, just as it is never far from the events of my life. Nonetheless God respects my freedom and (I suspect) values freedom in the rest of creation as well.”

This is how evolution and creationism are compatible. This idea that "God’s spirit guides the progression of life" is the view that major scientific organizations and the NCSE endorse as being compatible with science.

[Photo Credit: Francis Collins discusses “The Language of God”]

Saturday, May 02, 2009

What American Science Teachers Can't Say

John Pieret is a ~~pain in the~~ lawyer. He has something to say about a recent court case [Accommodating the Law].

The latest ruling on the religion-science front is by a Federal judge in California holding that a public school teacher who called creationism "religious, superstitious nonsense," violated a creationist student's First Amendment rights.

Since John has been following the debate on the blogs, he realizes the implications.

The lesson is not restricted to such blatant cases, however. It is clear that a government teacher could not teach that philosophical naturalism is true, as that would clearly render most religions false. And it is more than doubtful that a public school teacher could teach that science was true while, at the same time maintaining that it was in conflict with most religions, since that which is in conflict with the truth is, necessarily, false.

This is pretty much what I thought. High school science teachers cannot say that the deluge never happened and they cannot say that the idea of a 10,000 year-old Earth is wrong.¹ That would violate the American Constitution.

God Bless America.

1. I don't understand how they can get away with saying that evolution is true, since that statement is logically equivalent to saying that many forms of creationism are superstitious nonsense.

The Accommodationist Postion in Academic Matters

Margaret Somerville has written an essay on Facing up to the dangers of the intolerant university: Bird on an ethics wire. It is published in Academic Matters, the publication of the Ontario Confederation of University Faculty Associations (OCUFA).

Here's her brief biography as published in the journal.

Margaret Somerville is Samuel Gale Professor in the Faculty of Law and a professor in the Faculty of Medicine at McGill University and is the founding director of the McGill Centre for Medicine, Ethics and Law. In 2004, she received the UNESCO Avicenna Prize for Ethics in Science and in 2006 delivered the prestigious Massey Lectures.

I agree with a lot of what Somerville has to say about rampant political correctness in the universities.

That is where political correctness enters the picture. It excludes politically incorrect values from the “all values are equal” stable. The intense moral relativists will tolerate all values except those they deem to be politically incorrect—which just happen to be the ones that conflict with their values.

Political correctness operates by shutting down non-politically correct people’s freedom of speech. Anyone who challenges the politically correct stance is, thereby, automatically labeled as intolerant, a bigot, or hatemonger. The substance of their arguments against a politically correct stance is not addressed; rather people labeled as politically incorrect are, themselves, attacked as being intolerant and hateful simply for making those arguments. This derogatorily -label-the-person-and-dismiss-them-on-the-basis-of-that-label approach is intentionally used as a strategy to suppress strong arguments against any politically correct stance and, also, to avoid dealing with the substance of these arguments.

However, I also agree with Jeffrey Shallit that she applies her own standards inconsistently, such as when she insists that physicians are being "forced" to act against their conscience when treating certain patients [Margaret Somerville in "Academic Matters"].

Shallit is an expert on the difference between real free speech and its imposters.

I'd like to focus on another part of Somerville's essay.

Sixth, not only can we, but we must, cross the secular/religious divide, the science/religion divide and the divide between religions, if we are to find a shared ethics. This is where I believe both the fundamentalist religious people and the fundamentalist neo-atheists are wrong because they demand that we choose between religion and science. We must accommodate both.

Some would like to reduce religion to being seen as nothing more than a personal fantasy or superstition. But that’s not realistic. At best it will fail; at worst it will do serious harm because it will exacerbate the acrimony of the values conflicts and make it more likely, not less likely, that religion will become a focus of serious conflict. Also, because culture and religion are linked, even within democratic, multicultural, pluralistic Western societies, it will increase the number and intensity of the current values clashes and may contribute to culture wars.

I'm not sure what this means. I believe that religion is a superstition and I advocate a non-religious society. According to Somerville the "best" thing that could happen is that I will fail to convince people. The worst thing that will happen is that I will succeed but the result will make religion the focus of serious conflict. What a strange choice. The second option is exactly my goal.

I suppose the politically correct thing to do is to accommodate because we certainly can't have a situation where religion is challenged, can we?

Somerville says that religion and culture are linked. That's correct. It's an attitude that I want to change and there's lots of evidence that it is changing in other countries. Did this lead to "culture wars"? Yes, it did in some places—notably the Canadian province of Quebec in the 1960's. What Somerville fails to address is whether the culture wars are a good thing or a bad thing. She seems to be implying that we should not criticize religion because religious people might be upset. Don't we have a word for that kind of thinking?

[Photo Credit: The Catholic Registrar]

Vanier Canada Graduate Scholarships

There are 166 winners of Vanier Canada Graduate Scholarships. Of these, 34 are from the University of Toronto and several will be in the labs of my close colleagues. Congratulations to all the winners.

The scholarships will be administered by the three granting councils and each one is worth an astonishing $50,000 per year. That means that these scholarships amount to twice the level of funding of a typical graduate student at my university.

There's no sound logic behind awarding such a sum. T. Ryan Gregory points out that if the scholarships had been for $25,000 per year, the excess could have funded 73 research grants at an average of $34,000 per year. I agree that this money could have been better spent.

Gary Goodyear Explains Canada's Science Policy

Gary Goodyear, you might recall, is Canada's Minster of State (Science and Technology). He is a chiropractor who doesn't accept the scientific view of evolution.

The policy of the Conservative Party is to cut funding to the major granting agencies (SSHRC, NSERC, CIHR) by $148 million over the next few years. This will have a disastrous effect on basic research in Canada.

At a recent meeting in Washington (USA), Goodyear explained how Conservative ideology is driving science funding [Canadian research may hold key to ‘clean coal:' Goodyear].

Only days after Mr. Obama delighted America's scientific community by saying the “days of science taking a back seat to ideology are over” – a clear reference to the eight years George W. Bush was president – Mr. Goodyear made a point of claiming Canada's Conservative government took science seriously.

“Canada sees the role of science and technology in contributing to global economic growth and recovery,” he said. “We know that the jobs of tomorrow are found in the discoveries of today, so we look at research funding as investment — investment in innovation, in scientific discovery, in job creation, and as a hedge against tough economic conditions.”

But he also said the government's role in funding science went beyond backing pure research. Ottawa's science spending reflects “our government's emphasis on commercializing research and improving the processes that help get innovative ideas to the marketplace,” Mr. Goodyear told a two-day AAAS forum on science and technology.

“Commercialization is one area in which public policy makers play a huge role in enabling the private sector to do what it does best — turn knowledge into innovation, and innovation into greater wealth and well-being for people.”

I wish I were an American. President Obama seems to know the difference between science and technology and he seems to understand where real creativity and innovation can be found—it's not in technology development, it's in curiosity motivated basic research.

Friday, May 01, 2009

Don't Like Evolution in Alberta?

Let's say you live in Alberta and you oppose evolution because it conflicts with your religion. Is this a problem if your kids attend public school?

Maybe it is right now but if the Alberta government passes its new bill you will be able to take your kids out of class whenever evolution is discussed [Evolution classes optional under proposed Alberta law].

"This government supports a very, very fundamental right and that is parental rights with respect to education," said Premier Ed Stelmach.

Although Stelmach has confirmed the bill will give parents the authority to exclude their kids from classes if the topic of evolution comes up, Education Minister Dave Hancock said it won't change anything.

"With respect to values, religion and sex education have always been areas of concern for parents, and they've always been areas parents have had the right to be notified about and to exempt their students from," Hancock said.

I can't imagine why a parent would want to keep their children from learning about evolution. Are they so insecure about the strength of their religion that a lesson or two about evolution could turn their children into atheists?

Hopefully, this bill won't pass without being amended. If it does, then Alberta will look even more like some of the hick states in the USA that have tried to ban evolution in the schools.

Nobel Laureate: Paul Ehrlich

The Nobel Prize in Physiology or Medicine 1908

"in recognition of their work on immunity"

Paul Ehrlich (1854 - 1915) won the Noble Prize in 1908 for his contributions to understanding immunology. His co-recipient was Ilya Ilyich Mechnikov.

Ehrlich was already a well-known scientist at the time he received that Nobel Prize and he subsequently went on to achieve even greater fame for synthesizing a drug to treat syphilis [Monday's Molecule #119].

Although Ehrlich's specific contributions to immunology aren't mentioned in the presentation speech, they mostly concern the discovery of antibodies. Here's how his contribution is described ...
THEME:
Nobel Laureates

An endless series of questions now arises: Why are antibodies only built up against some substances and not against all substances which are foreign to the organism? Where are the antibodies formed? By what process are they formed? What is the nature and constitution of these antibodies? How do they react on the microorganisms and their poisons? And various other questions which are important as regards the development and practical utilization of the theory of immunity. It is also a matter of great interest that connecting links have been found between the theory of immunity and the normal physiological processes.

A great deal of intensive and very fruitful work has been devoted to these questions in the last one and a half decades. A large number of research scientists have served the cause of science well by their discoveries and achievements. It is not possible here to report on the extent to which the questions have been answered, neither is it possible to describe the separate accomplishments of individual scientists in this field.

A man who has been responsible for important scientific progress as organizer and leader in this field deserves to be mentioned among the first of those who have dedicated themselves to a study of immunity, is the research scientist Paul Ehrlich, already famous for his other biological work, and the Professorial Staff of the Caroline Institute wishes to honour him too with this year's Nobel Prize for his work in the sphere of immunity.

[Photo Credit: Wellcome Trust Photographic Library]

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

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Quotations

The old argument of design in nature, as given by Paley, which formerly
seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We
can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by
an intellignet being, like the hinge of a door by man. There seems to be no more design in the
variability of organic beings and in the action of natural selection, than in the course which the wind
blows.

Charles Darwin (c1880)

Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles
Darwin (1859)

Science reveals where religion conceals. Where religion
purports to explain, it actually resorts to tautology. To assert that "God did it" is no
more than an admission of ignorance dressed deceitfully as an explanation..

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)

I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339

The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)

Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)

Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335

The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84